Header list of 1jtw.pdb file
Complete list - 23 20 Bytes
HEADER RNA 22-AUG-01 1JTW TITLE STRUCTURE OF SL4 RNA FROM THE HIV-1 PACKAGING SIGNAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*GP*UP*GP*CP*GP*AP*GP*AP*GP*CP*GP*UP*CP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HIV-1 PACKAGING SIGNAL SL4 HAIRPIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS IN THE PACKAGING SIGNAL OF HIV- SOURCE 4 1. KEYWDS HAIRPIN, TANDEM G-U PAIRS, GAGA TETRALOOPS, RNA EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR D.J.KERWOOD,M.J.CAVALUZZI,P.N.BORER REVDAT 3 23-FEB-22 1JTW 1 REMARK LINK ATOM REVDAT 2 24-FEB-09 1JTW 1 VERSN REVDAT 1 12-DEC-01 1JTW 0 JRNL AUTH D.J.KERWOOD,M.J.CAVALUZZI,P.N.BORER JRNL TITL STRUCTURE OF SL4 RNA FROM THE HIV-1 PACKAGING SIGNAL. JRNL REF BIOCHEMISTRY V. 40 14518 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11724565 JRNL DOI 10.1021/BI0111909 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 DYANA STRUCTURES WERE FURTHER REFINED WITH THE REMARK 3 MOLECULAR DYNAMICS AND MINIMIZATION PROGRAM, AMBER. REMARK 4 REMARK 4 1JTW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014179. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : ~0.7MM SL4 CONCENTRATION IN REMARK 210 BUFFER: 25MM NACL, 5MM NAHPO4 REMARK 210 (PH 7.0), 0.1MM EDTA, 0.01% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 5 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SODIUM IONS WHICH WERE DISTANT FROM THE RNA WERE REMOVED. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 8 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 10 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 11 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 12 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 12 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 12 A A 16 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 13 G A 2 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 13 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 14 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 14 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 14 A A 16 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 7 0.07 SIDE CHAIN REMARK 500 1 G A 11 0.06 SIDE CHAIN REMARK 500 2 G A 7 0.10 SIDE CHAIN REMARK 500 2 C A 15 0.06 SIDE CHAIN REMARK 500 3 G A 7 0.07 SIDE CHAIN REMARK 500 3 G A 9 0.05 SIDE CHAIN REMARK 500 4 G A 1 0.06 SIDE CHAIN REMARK 500 4 G A 7 0.12 SIDE CHAIN REMARK 500 4 C A 15 0.07 SIDE CHAIN REMARK 500 5 G A 7 0.08 SIDE CHAIN REMARK 500 5 G A 9 0.07 SIDE CHAIN REMARK 500 6 G A 5 0.07 SIDE CHAIN REMARK 500 6 G A 7 0.05 SIDE CHAIN REMARK 500 7 G A 2 0.05 SIDE CHAIN REMARK 500 7 G A 7 0.09 SIDE CHAIN REMARK 500 7 G A 11 0.06 SIDE CHAIN REMARK 500 8 G A 5 0.05 SIDE CHAIN REMARK 500 8 G A 7 0.08 SIDE CHAIN REMARK 500 9 G A 5 0.06 SIDE CHAIN REMARK 500 9 G A 7 0.08 SIDE CHAIN REMARK 500 9 G A 11 0.06 SIDE CHAIN REMARK 500 9 C A 15 0.08 SIDE CHAIN REMARK 500 10 G A 2 0.06 SIDE CHAIN REMARK 500 10 G A 7 0.12 SIDE CHAIN REMARK 500 11 G A 2 0.06 SIDE CHAIN REMARK 500 11 U A 4 0.06 SIDE CHAIN REMARK 500 11 G A 7 0.06 SIDE CHAIN REMARK 500 11 C A 15 0.09 SIDE CHAIN REMARK 500 12 G A 7 0.08 SIDE CHAIN REMARK 500 12 A A 16 0.07 SIDE CHAIN REMARK 500 13 G A 2 0.06 SIDE CHAIN REMARK 500 13 G A 7 0.08 SIDE CHAIN REMARK 500 13 G A 11 0.07 SIDE CHAIN REMARK 500 13 C A 15 0.09 SIDE CHAIN REMARK 500 14 G A 5 0.08 SIDE CHAIN REMARK 500 14 G A 9 0.06 SIDE CHAIN REMARK 500 14 A A 16 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 27 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 2 OP2 REMARK 620 2 G A 3 OP2 146.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 18 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 3 O6 REMARK 620 2 U A 4 O4 76.5 REMARK 620 3 G A 13 O6 87.6 79.2 REMARK 620 4 U A 14 O4 79.7 143.4 72.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 19 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 3 OP1 REMARK 620 2 U A 4 OP2 148.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 20 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 4 OP1 REMARK 620 2 U A 4 O5' 52.6 REMARK 620 3 G A 5 OP2 149.5 97.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 22 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 7 OP1 REMARK 620 2 G A 7 OP2 52.1 REMARK 620 3 A A 8 OP1 134.5 149.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 24 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 8 OP2 REMARK 620 2 G A 9 OP2 116.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 25 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 OP1 REMARK 620 2 G A 9 O5' 50.8 REMARK 620 3 A A 10 OP2 152.9 102.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 26 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 OP1 REMARK 620 2 G A 11 OP2 56.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 29 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 O3' REMARK 620 2 C A 12 OP1 56.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 28 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 12 OP2 REMARK 620 2 G A 13 OP2 148.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 30 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 14 OP2 REMARK 620 2 U A 14 O5' 51.8 REMARK 620 3 C A 15 OP2 147.7 96.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 31 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 15 O5' REMARK 620 2 A A 16 OP2 102.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 20 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 28 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 29 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 30 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 31 DBREF 1JTW A 1 16 PDB 1JTW 1JTW 1 16 SEQRES 1 A 16 G G G U G C G A G A G C G SEQRES 2 A 16 U C A HET NA A 17 1 HET NA A 18 1 HET NA A 19 1 HET NA A 20 1 HET NA A 21 1 HET NA A 22 1 HET NA A 23 1 HET NA A 24 1 HET NA A 25 1 HET NA A 26 1 HET NA A 27 1 HET NA A 28 1 HET NA A 29 1 HET NA A 30 1 HET NA A 31 1 HETNAM NA SODIUM ION FORMUL 2 NA 15(NA 1+) LINK OP1 G A 2 NA NA A 17 1555 1555 2.49 LINK OP2 G A 2 NA NA A 27 1555 1555 2.73 LINK O6 G A 3 NA NA A 18 1555 1555 2.62 LINK OP1 G A 3 NA NA A 19 1555 1555 2.63 LINK OP2 G A 3 NA NA A 27 1555 1555 2.62 LINK O4 U A 4 NA NA A 18 1555 1555 2.74 LINK OP2 U A 4 NA NA A 19 1555 1555 2.54 LINK OP1 U A 4 NA NA A 20 1555 1555 2.63 LINK O5' U A 4 NA NA A 20 1555 1555 2.97 LINK OP2 G A 5 NA NA A 20 1555 1555 2.68 LINK OP1 C A 6 NA NA A 23 1555 1555 2.50 LINK OP1 G A 7 NA NA A 22 1555 1555 2.95 LINK OP2 G A 7 NA NA A 22 1555 1555 2.85 LINK OP1 A A 8 NA NA A 22 1555 1555 2.70 LINK OP2 A A 8 NA NA A 24 1555 1555 2.60 LINK OP2 G A 9 NA NA A 24 1555 1555 2.56 LINK OP1 G A 9 NA NA A 25 1555 1555 2.85 LINK O5' G A 9 NA NA A 25 1555 1555 2.94 LINK OP2 A A 10 NA NA A 25 1555 1555 2.62 LINK OP1 G A 11 NA NA A 26 1555 1555 2.72 LINK OP2 G A 11 NA NA A 26 1555 1555 2.61 LINK O3' G A 11 NA NA A 29 1555 1555 2.62 LINK OP2 C A 12 NA NA A 28 1555 1555 2.69 LINK OP1 C A 12 NA NA A 29 1555 1555 2.66 LINK O6 G A 13 NA NA A 18 1555 1555 2.59 LINK OP2 G A 13 NA NA A 28 1555 1555 2.56 LINK O4 U A 14 NA NA A 18 1555 1555 2.90 LINK OP1 U A 14 NA NA A 21 1555 1555 2.58 LINK OP2 U A 14 NA NA A 30 1555 1555 2.66 LINK O5' U A 14 NA NA A 30 1555 1555 2.99 LINK OP2 C A 15 NA NA A 30 1555 1555 2.54 LINK O5' C A 15 NA NA A 31 1555 1555 2.89 LINK OP2 A A 16 NA NA A 31 1555 1555 2.59 SITE 1 AC1 1 G A 2 SITE 1 AC2 4 G A 3 U A 4 G A 13 U A 14 SITE 1 AC3 2 G A 3 U A 4 SITE 1 AC4 2 U A 4 G A 5 SITE 1 AC5 2 G A 13 U A 14 SITE 1 AC6 2 G A 7 A A 8 SITE 1 AC7 1 C A 6 SITE 1 AC8 3 G A 7 A A 8 G A 9 SITE 1 AC9 3 G A 7 G A 9 A A 10 SITE 1 BC1 2 A A 10 G A 11 SITE 1 BC2 2 G A 2 G A 3 SITE 1 BC3 2 C A 12 G A 13 SITE 1 BC4 2 G A 11 C A 12 SITE 1 BC5 2 U A 14 C A 15 SITE 1 BC6 2 C A 15 A A 16 CRYST1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1
Complete list - 23 20 Bytes