Header list of 1r3x.pdb file
Complete list - 2 20 Bytes
HEADER DNA-RNA HYBRID 06-FEB-98 1R3X TITLE INTRAMOLECULAR DNA TRIPLEX WITH RNA THIRD STRAND, NMR, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 COMPND 6 AND BETWEEN T 16 AND U 17. C 18, C 20, AND C 22 ARE PROTONATED AT N3; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*TP*CP*TP*CP*TP*CP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 COMPND 12 AND BETWEEN T 16 AND U 17. C 18, C 20, AND C 22 ARE PROTONATED AT N3; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: RNA (5'-R(*UP*CP*UP*CP*UP*CP*UP*U)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 COMPND 18 AND BETWEEN T 16 AND U 17. C 18, C 20, AND C 22 ARE PROTONATED AT N3 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS OLIGONUCLEOTIDE, TRIPLEX, RNA THIRD STRAND, DNA-RNA COMPLEX, DNA-RNA KEYWDS 2 HYBRID EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.H.GOTFREDSEN,P.SCHULTZE,J.FEIGON REVDAT 3 02-MAR-22 1R3X 1 REMARK REVDAT 2 24-FEB-09 1R3X 1 VERSN REVDAT 1 20-MAY-98 1R3X 0 JRNL AUTH C.H.GOTFREDSEN,P.SCHULTZE,J.FEIGON JRNL TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR JRNL TITL 2 PYRIMIDINE-PURINE-PYRIMIDINE TRIPLEX CONTAINING AN RNA THIRD JRNL TITL 3 STRAND JRNL REF J.AM.CHEM.SOC. V. 120 4281 1998 JRNL REFN ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LAST REFINEMENT STEP USED RELAXATION REMARK 3 MATRIX REFINEMENT. REMARK 4 REMARK 4 1R3X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175955. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; TOCSY-NOESY; HSQC; REMARK 210 DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX500; AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY/ SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST OVERALL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O6 DG A 4 H41 C C 20 1.31 REMARK 500 O6 DG A 2 H41 DC B 15 1.51 REMARK 500 N7 DG A 2 O2 C C 18 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DG A 2 C2' DG A 2 C1' 0.069 REMARK 500 1 DG A 2 C8 DG A 2 N9 -0.050 REMARK 500 1 DA A 3 C8 DA A 3 N9 -0.062 REMARK 500 1 DA A 5 N9 DA A 5 C4 -0.046 REMARK 500 1 DA A 8 C8 DA A 8 N9 -0.058 REMARK 500 1 DA A 8 N9 DA A 8 C4 -0.046 REMARK 500 1 DT B 9 C5 DT B 9 C6 -0.043 REMARK 500 1 DT B 9 C6 DT B 9 N1 -0.066 REMARK 500 1 DT B 10 C6 DT B 10 N1 -0.046 REMARK 500 1 DC B 11 C5' DC B 11 C4' 0.053 REMARK 500 1 DT B 12 C5' DT B 12 C4' 0.051 REMARK 500 1 DT B 12 C3' DT B 12 C2' -0.074 REMARK 500 1 DT B 12 C6 DT B 12 N1 -0.050 REMARK 500 1 DT B 12 C5 DT B 12 C7 -0.056 REMARK 500 1 DC B 13 C3' DC B 13 C2' 0.089 REMARK 500 1 DT B 14 C5 DT B 14 C6 -0.049 REMARK 500 1 DT B 14 C6 DT B 14 N1 -0.079 REMARK 500 1 DT B 14 C5 DT B 14 C7 -0.059 REMARK 500 1 C C 18 C2' C C 18 C1' -0.051 REMARK 500 1 C C 20 N3 C C 20 C4 0.046 REMARK 500 2 DG A 2 C4' DG A 2 C3' 0.062 REMARK 500 2 DG A 2 C2' DG A 2 C1' 0.077 REMARK 500 2 DA A 5 N9 DA A 5 C4 -0.047 REMARK 500 2 DA A 8 N9 DA A 8 C4 -0.061 REMARK 500 2 DT B 9 C6 DT B 9 N1 -0.054 REMARK 500 2 DT B 10 C6 DT B 10 N1 -0.043 REMARK 500 2 DT B 12 C3' DT B 12 C2' -0.072 REMARK 500 2 DT B 12 C6 DT B 12 N1 -0.050 REMARK 500 2 DT B 12 C5 DT B 12 C7 -0.060 REMARK 500 2 DC B 13 C3' DC B 13 C2' 0.081 REMARK 500 2 DT B 14 C5' DT B 14 C4' 0.058 REMARK 500 2 DT B 14 C6 DT B 14 N1 -0.076 REMARK 500 2 DT B 14 C5 DT B 14 C7 -0.070 REMARK 500 2 DC B 15 C5' DC B 15 C4' 0.047 REMARK 500 3 DG A 2 C2' DG A 2 C1' 0.076 REMARK 500 3 DG A 2 C8 DG A 2 N9 -0.051 REMARK 500 3 DA A 3 C8 DA A 3 N9 -0.064 REMARK 500 3 DA A 5 N9 DA A 5 C4 -0.040 REMARK 500 3 DA A 8 C8 DA A 8 N9 -0.050 REMARK 500 3 DA A 8 N9 DA A 8 C4 -0.045 REMARK 500 3 DT B 9 C6 DT B 9 N1 -0.060 REMARK 500 3 DT B 10 C6 DT B 10 N1 -0.044 REMARK 500 3 DC B 11 C5' DC B 11 C4' 0.060 REMARK 500 3 DC B 11 C3' DC B 11 C2' 0.078 REMARK 500 3 DT B 12 C5' DT B 12 C4' 0.046 REMARK 500 3 DT B 12 C3' DT B 12 C2' -0.054 REMARK 500 3 DT B 12 C6 DT B 12 N1 -0.052 REMARK 500 3 DT B 12 C5 DT B 12 C7 -0.063 REMARK 500 3 DC B 13 C3' DC B 13 C2' 0.078 REMARK 500 3 DC B 13 C2' DC B 13 C1' 0.080 REMARK 500 REMARK 500 THIS ENTRY HAS 175 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 1 DA A 1 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG A 2 C4' - C3' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DA A 3 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DA A 3 N9 - C1' - C2' ANGL. DEV. = -28.4 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 13.7 DEGREES REMARK 500 1 DA A 3 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 4 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 4 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG A 4 C3' - C2' - C1' ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = -8.9 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 4 C3' - O3' - P ANGL. DEV. = 11.7 DEGREES REMARK 500 1 DA A 5 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DA A 5 C5 - N7 - C8 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 5 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 10.8 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DA A 7 C5' - C4' - O4' ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DA A 7 C1' - O4' - C4' ANGL. DEV. = -8.6 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 7 C6 - N1 - C2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA A 8 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 9 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT B 9 C4 - C5 - C6 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 9 C4 - C5 - C7 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DT B 9 C6 - C5 - C7 ANGL. DEV. = -10.9 DEGREES REMARK 500 1 DT B 10 C5' - C4' - O4' ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DT B 10 C4' - C3' - O3' ANGL. DEV. = 13.0 DEGREES REMARK 500 1 DT B 10 O4' - C1' - C2' ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DT B 10 C5 - C4 - O4 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DT B 10 C4 - C5 - C7 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DT B 10 C6 - C5 - C7 ANGL. DEV. = -11.2 DEGREES REMARK 500 1 DT B 10 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DC B 11 O3' - P - O5' ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DC B 11 O4' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 1 DC B 11 C5' - C4' - O4' ANGL. DEV. = 13.3 DEGREES REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DT B 12 O4' - C4' - C3' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT B 12 C5' - C4' - O4' ANGL. DEV. = 9.7 DEGREES REMARK 500 1 DT B 12 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DT B 12 C4' - C3' - O3' ANGL. DEV. = 17.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 801 ANGLE DEVIATIONS. 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 4 DC B 13 0.06 SIDE CHAIN REMARK 500 6 DC B 13 0.06 SIDE CHAIN REMARK 500 10 DC B 13 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1R3X A 1 8 PDB 1R3X 1R3X 1 8 DBREF 1R3X B 9 16 PDB 1R3X 1R3X 9 16 DBREF 1R3X C 17 24 PDB 1R3X 1R3X 17 24 SEQRES 1 A 8 DA DG DA DG DA DG DA DA SEQRES 1 B 8 DT DT DC DT DC DT DC DT SEQRES 1 C 8 U C U C U C U U CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 - 2 20 Bytes