Header list of 1n8x.pdb file
Complete list - b 23 2 Bytes
HEADER RNA 21-NOV-02 1N8X
TITLE SOLUTION STRUCTURE OF HIV-1 STEM LOOP SL1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HIV-1 STEM LOOP SL1 MONOMERIC RNA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: HIV-1 STEM LOOP SL1;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY IN VITRO
SOURCE 4 TRANSCRIPTION USING A SINGLE STRANDED DNA TEMPLATE AND T7 RNA
SOURCE 5 POLYMERASE.
KEYWDS HIV, SL1, RNA STEM LOOP, BULGE, G-A MISMATCH, RNA
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR D.C.LAWRENCE,C.C.STOVER,J.NOZNITSKY,Z.WU,M.F.SUMMERS
REVDAT 4 23-FEB-22 1N8X 1 REMARK
REVDAT 3 24-FEB-09 1N8X 1 VERSN
REVDAT 2 15-APR-03 1N8X 1 JRNL
REVDAT 1 08-APR-03 1N8X 0
JRNL AUTH D.C.LAWRENCE,C.C.STOVER,J.NOZNITSKY,Z.WU,M.F.SUMMERS
JRNL TITL STRUCTURE OF THE INTACT STEM AND BULGE OF HIV-1 PSI-RNA
JRNL TITL 2 STEM-LOOP SL1
JRNL REF J.MOL.BIOL. V. 326 529 2003
JRNL REFN ISSN 0022-2836
JRNL PMID 12559920
JRNL DOI 10.1016/S0022-2836(02)01305-0
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, DYANA 1.5
REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, MUMENTHALER, WUTHRICH
REMARK 3 (DYANA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 408 EXPERIMENTAL RESTRAINTS,
REMARK 3 INCLUDING 298 NOE-DERIVED DISTANCE RESTRAINTS, 84 HYDROGEN BOND
REMARK 3 RESTRAINTS,
REMARK 3 AND 26 DIPOLAR COUPLING RESTRAINTS.
REMARK 4
REMARK 4 1N8X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-03.
REMARK 100 THE DEPOSITION ID IS D_1000017666.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308; 308
REMARK 210 PH : 7.0; 8.0
REMARK 210 IONIC STRENGTH : NULL; 10 MM TRIS-CL, 0.1 MM NA
REMARK 210 -EDTA
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM SL1 MONOMERIC RNA, U
REMARK 210 -15N,13C; 100% D2O; 1 MM SL1
REMARK 210 MONOMERIC RNA, CYT-15N,13C; 100%
REMARK 210 D2O; 1 MM SL1 MONOMERIC RNA, GUA-
REMARK 210 15N,13C; 100% D2O; 1 MM SL1
REMARK 210 MONOMERIC RNA, GUA-15N,13C; 10
REMARK 210 MM TRIS-D11, PH 8.0, 0.1 MM EDTA;
REMARK 210 18 MG/ML PF1 BACTERIOPHAGE
REMARK 210 (ASLA); 100% D2O; 1 MM SL1
REMARK 210 MONOMERIC RNA, UNLABELED; 100%
REMARK 210 D2O; 1 MM SL1 MONOMERIC RNA, GUA-
REMARK 210 15N,13C; 10 MM TRIS-D11, PH 8.0,
REMARK 210 0.1 MM EDTA; 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 4D_13C
REMARK 210 -SEPARATED_NOESY; 3D_13C-
REMARK 210 SEPARATED_ROESY; IPAP H-COUPLED
REMARK 210 CT-HSQC; 2D NOESY; 2D ROESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.0.3
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 600
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 EXPERIMENT 8 (IPAP H-COUPLED CT-HSQC) WAS PERFORMED ON SAMPLE 4
REMARK 210 AND SAMPLE 6 (GUA-15N,13C-LABELED SL1 WITH AND WITHOUT PF1 PHAGE).
REMARK 210 THE DIFFERENCE BETWEEN THE J-COUPLING VALUES = DIPOLAR COUPLING
REMARK 210 VALUE FOR A GIVEN C-H BOND.
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: 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
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 G A 1 O4' G A 1 C4' -0.175
REMARK 500 1 G A 12 O4' G A 12 C4' -0.125
REMARK 500 1 G A 26 O4' G A 26 C4' -0.090
REMARK 500 2 G A 1 O4' G A 1 C4' -0.179
REMARK 500 2 G A 2 O4' G A 2 C4' -0.079
REMARK 500 2 G A 12 O4' G A 12 C4' -0.123
REMARK 500 2 G A 26 O4' G A 26 C4' -0.089
REMARK 500 3 G A 1 O4' G A 1 C4' -0.179
REMARK 500 3 G A 12 O4' G A 12 C4' -0.095
REMARK 500 3 G A 18 O4' G A 18 C4' -0.213
REMARK 500 3 G A 26 O4' G A 26 C4' -0.091
REMARK 500 4 G A 1 O4' G A 1 C4' -0.185
REMARK 500 4 G A 12 O4' G A 12 C4' -0.084
REMARK 500 4 G A 18 O4' G A 18 C4' -0.315
REMARK 500 4 G A 26 O4' G A 26 C4' -0.137
REMARK 500 5 G A 1 O4' G A 1 C4' -0.175
REMARK 500 5 G A 2 O4' G A 2 C4' -0.130
REMARK 500 5 G A 12 O4' G A 12 C4' -0.113
REMARK 500 5 G A 18 O4' G A 18 C4' -0.084
REMARK 500 5 G A 26 O4' G A 26 C4' -0.097
REMARK 500 6 G A 1 O4' G A 1 C4' -0.205
REMARK 500 6 G A 12 O4' G A 12 C4' -0.102
REMARK 500 6 G A 26 O4' G A 26 C4' -0.091
REMARK 500 6 G A 29 O4' G A 29 C4' -0.087
REMARK 500 7 G A 1 O4' G A 1 C4' -0.149
REMARK 500 7 G A 12 O4' G A 12 C4' -0.107
REMARK 500 7 G A 29 O4' G A 29 C4' -0.079
REMARK 500 8 G A 1 O4' G A 1 C4' -0.186
REMARK 500 8 G A 12 O4' G A 12 C4' -0.120
REMARK 500 8 C A 36 O4' C A 36 C4' -0.191
REMARK 500 9 G A 1 O4' G A 1 C4' -0.172
REMARK 500 9 G A 12 O4' G A 12 C4' -0.119
REMARK 500 9 G A 18 O4' G A 18 C4' -0.272
REMARK 500 9 G A 26 O4' G A 26 C4' -0.093
REMARK 500 10 G A 1 O4' G A 1 C4' -0.139
REMARK 500 10 G A 12 O4' G A 12 C4' -0.164
REMARK 500 10 G A 18 O4' G A 18 C4' -0.269
REMARK 500 11 G A 1 O4' G A 1 C4' -0.160
REMARK 500 11 G A 12 O4' G A 12 C4' -0.098
REMARK 500 11 G A 18 O4' G A 18 C4' -0.259
REMARK 500 11 G A 26 O4' G A 26 C4' -0.132
REMARK 500 12 G A 1 O4' G A 1 C4' -0.117
REMARK 500 12 G A 12 O4' G A 12 C4' -0.128
REMARK 500 12 G A 26 O4' G A 26 C4' -0.084
REMARK 500 13 G A 1 O4' G A 1 C4' -0.168
REMARK 500 13 G A 12 O4' G A 12 C4' -0.093
REMARK 500 13 G A 29 O4' G A 29 C4' -0.097
REMARK 500 14 G A 1 O4' G A 1 C4' -0.125
REMARK 500 14 G A 12 O4' G A 12 C4' -0.112
REMARK 500 14 A A 27 O4' A A 27 C4' -0.088
REMARK 500
REMARK 500 THIS ENTRY HAS 74 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 G A 1 C5' - C4' - O4' ANGL. DEV. = 9.8 DEGREES
REMARK 500 1 G A 1 C1' - O4' - C4' ANGL. DEV. = 10.1 DEGREES
REMARK 500 1 G A 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 G A 2 O4' - C4' - C3' ANGL. DEV. = -8.0 DEGREES
REMARK 500 1 G A 2 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 1 G A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 A A 3 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES
REMARK 500 1 A A 3 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 A A 3 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 C A 4 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES
REMARK 500 1 C A 4 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 U A 5 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES
REMARK 500 1 U A 5 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 C A 6 O4' - C4' - C3' ANGL. DEV. = -7.5 DEGREES
REMARK 500 1 C A 6 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 G A 7 O4' - C4' - C3' ANGL. DEV. = -8.2 DEGREES
REMARK 500 1 G A 7 C5' - C4' - O4' ANGL. DEV. = -7.5 DEGREES
REMARK 500 1 G A 7 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 1 G A 7 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 7 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 7 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 G A 8 O4' - C4' - C3' ANGL. DEV. = -6.9 DEGREES
REMARK 500 1 G A 8 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 G A 8 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 8 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 8 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 C A 9 O4' - C4' - C3' ANGL. DEV. = -7.2 DEGREES
REMARK 500 1 C A 9 C5' - C4' - O4' ANGL. DEV. = 15.7 DEGREES
REMARK 500 1 C A 9 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 U A 10 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 U A 10 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 U A 11 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 U A 11 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 G A 12 C5' - C4' - O4' ANGL. DEV. = 22.1 DEGREES
REMARK 500 1 G A 12 C1' - O4' - C4' ANGL. DEV. = 8.5 DEGREES
REMARK 500 1 G A 12 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 12 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 12 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 C A 13 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 C A 13 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 C A 13 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 U A 14 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES
REMARK 500 1 U A 14 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 U A 14 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 G A 15 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES
REMARK 500 1 G A 15 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 2478 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 999
REMARK 999 SEQUENCE AUTHOR STATES THERE ARE THREE ADDITIONAL BASES ON THE 5'
REMARK 999 AND 3' ENDS, WHICH FORM WC BASE PAIRS: 5'-GGA ... UCC-3' DIS
REMARK 999 LOOP (AAGCGCGCA) REPLACED WITH GAGA TETRALOOP' MONOMERIC RNA
REMARK 999 ENGINEERED BY REPLACING THE TERMINAL LOOP WITH A GAGA TETRALOOP.
REMARK 999 LOWER STEM HAS AN ADDITIONAL THREE BASE PAIRS: 5'GGA...UCC3'.
REMARK 999 RESIDUES ARE NUMBERED 1 THROUGH 36 IN COORDINATE FILE ALTHOUGH
REMARK 999 THEY ARE NUMBERED DIFFERENTLY IN ARTICLE. INTERNAL BULGED LOOP
REMARK 999 COMPOSED OF G5 (5' STRAND), A24, G25, AND G26 (3' STRAND) IS
REMARK 999 STRUCTURED WITH A G5-A24 MISMATCH AND G25, G26 STACKING UNDER
REMARK 999 A24.
DBREF 1N8X A 1 36 PDB 1N8X 1N8X 1 36
SEQRES 1 A 36 G G A C U C G G C U U G C
SEQRES 2 A 36 U G G A G A C G G C A A G
SEQRES 3 A 36 A G G C G A G U C C
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 - b 23 2 Bytes