10 20 30 40 50 60 70 80 2DI2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER METAL BINDING PROTEIN 27-MAR-06 2DI2
TITLE NMR STRUCTURE OF THE HIV-2 NUCLEOCAPSID PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN P7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUS 1-29; COMPND 5 SYNONYM: HIV-2 NUCLEOCAPSID PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE HAS BEEN CHEMICALLY SYNTHESIZED
KEYWDS NUCLEOCAPSID PROTEIN, HIV-2, RNA RECOGNITION, ZINC FINGER, KEYWDS 2 MUTANT, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 13
AUTHOR T.MATSUI,Y.KODERA,H.ENDOH,E.MIYAUCHI,H.KOMATSU,K.SATO, AUTHOR 2 T.TANAKA,T.KOHNO,T.MAEDA
REVDAT 3 24-FEB-09 2DI2 1 VERSN REVDAT 2 17-APR-07 2DI2 1 REMARK REVDAT 1 13-MAR-07 2DI2 0
JRNL AUTH T.MATSUI,Y.KODERA,H.ENDOH,E.MIYAUCHI,H.KOMATSU, JRNL AUTH 2 K.SATO,T.TANAKA,T.KOHNO,T.MAEDA JRNL TITL RNA RECOGNITION MECHANISM OF THE MINIMAL ACTIVE JRNL TITL 2 DOMAIN OF THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2 JRNL TITL 3 NUCLEOCAPSID PROTEIN JRNL REF J.BIOCHEM.(TOKYO) V. 141 269 2007 JRNL REFN ISSN 0021-924X JRNL PMID 17202191 JRNL DOI 10.1093/JB/MVM037
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR-NIH 2.9.9 REMARK 3 AUTHORS : SCHWIETERS C.D. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2DI2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB025438.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5MM PROTEIN; 5.5MM ZNCL2; 95% REMARK 210 H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D TOCSY, 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR-NIH 2.9.9 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLN A 2 -67.80 -102.92 REMARK 500 1 GLN A 3 65.86 -162.61 REMARK 500 1 ARG A 4 -91.17 59.16 REMARK 500 1 VAL A 6 166.69 -47.88 REMARK 500 1 CYS A 9 78.55 31.89 REMARK 500 1 CYS A 12 -53.94 -127.51 REMARK 500 1 CYS A 22 100.52 -47.17 REMARK 500 1 ARG A 26 104.54 50.86 REMARK 500 1 ARG A 27 92.91 59.82 REMARK 500 1 GLN A 28 -61.70 -178.58 REMARK 500 2 GLN A 2 77.54 -108.74 REMARK 500 2 ARG A 4 -160.55 47.05 REMARK 500 2 LYS A 5 -155.13 -131.39 REMARK 500 2 VAL A 6 -175.57 -46.63 REMARK 500 2 ARG A 8 47.50 -82.80 REMARK 500 2 CYS A 9 83.79 30.37 REMARK 500 2 CYS A 12 -42.61 -138.84 REMARK 500 2 PRO A 25 49.27 -77.84 REMARK 500 2 ARG A 26 166.18 55.22 REMARK 500 2 ARG A 27 22.60 47.81 REMARK 500 3 GLN A 2 36.38 -171.62 REMARK 500 3 ARG A 4 156.35 -36.70 REMARK 500 3 LYS A 5 -177.72 -67.11 REMARK 500 3 VAL A 6 -173.44 -52.03 REMARK 500 3 ARG A 8 36.75 -84.25 REMARK 500 3 CYS A 9 83.10 39.16 REMARK 500 3 CYS A 12 -75.91 -127.30 REMARK 500 3 PRO A 25 34.31 -81.89 REMARK 500 3 ARG A 26 84.02 60.35 REMARK 500 3 GLN A 28 17.64 -145.73 REMARK 500 4 GLN A 3 -138.46 -135.44 REMARK 500 4 ARG A 4 -12.06 77.37 REMARK 500 4 LYS A 5 -174.43 59.87 REMARK 500 4 VAL A 6 -179.40 61.64 REMARK 500 4 ARG A 8 46.05 -78.95 REMARK 500 4 CYS A 9 85.98 23.84 REMARK 500 4 TRP A 10 -29.94 -39.86 REMARK 500 4 CYS A 12 -73.05 -141.50 REMARK 500 4 ARG A 26 123.93 68.02 REMARK 500 4 GLN A 28 64.69 -165.00 REMARK 500 5 GLN A 2 43.64 -86.82 REMARK 500 5 ARG A 4 112.93 166.42 REMARK 500 5 LYS A 5 53.44 -179.23 REMARK 500 5 CYS A 9 98.02 40.20 REMARK 500 5 CYS A 12 -57.48 -123.21 REMARK 500 5 CYS A 22 100.27 -43.94 REMARK 500 5 ARG A 26 101.62 55.40 REMARK 500 6 GLN A 2 -163.46 60.46 REMARK 500 6 ARG A 4 174.16 52.91 REMARK 500 6 VAL A 6 174.71 -46.79 REMARK 500 6 CYS A 9 100.80 30.25 REMARK 500 6 CYS A 22 100.64 -45.93 REMARK 500 6 ARG A 26 108.69 -51.02 REMARK 500 6 ARG A 27 -29.04 80.30 REMARK 500 7 ARG A 4 -165.08 45.61 REMARK 500 7 VAL A 6 171.21 -46.19 REMARK 500 7 ARG A 8 49.66 -79.08 REMARK 500 7 CYS A 9 98.99 39.35 REMARK 500 7 CYS A 22 78.55 -58.43 REMARK 500 7 ALA A 24 73.77 -119.70 REMARK 500 7 PRO A 25 56.61 -69.32 REMARK 500 7 ARG A 26 115.28 -1.81 REMARK 500 7 GLN A 28 89.64 46.61 REMARK 500 8 GLN A 2 -107.51 -91.46 REMARK 500 8 LYS A 5 57.61 179.40 REMARK 500 8 CYS A 9 89.10 48.34 REMARK 500 8 CYS A 12 -68.26 -121.99 REMARK 500 8 ARG A 26 155.63 64.11 REMARK 500 8 GLN A 28 47.26 38.54 REMARK 500 9 GLN A 3 -75.14 58.42 REMARK 500 9 ARG A 4 -80.96 74.17 REMARK 500 9 LYS A 5 65.19 158.26 REMARK 500 9 CYS A 9 79.63 41.62 REMARK 500 9 CYS A 12 -70.97 -117.21 REMARK 500 9 CYS A 22 107.14 -56.59 REMARK 500 9 GLN A 28 -42.66 -151.32 REMARK 500 10 GLN A 2 -98.54 -107.67 REMARK 500 10 GLN A 3 -34.96 177.53 REMARK 500 10 ARG A 4 -1.47 71.26 REMARK 500 10 CYS A 9 74.90 28.87 REMARK 500 10 TRP A 10 -28.58 -37.79 REMARK 500 10 CYS A 12 -70.19 -130.41 REMARK 500 10 CYS A 22 105.01 -55.53 REMARK 500 10 PRO A 25 55.95 -68.64 REMARK 500 10 ARG A 26 -165.76 39.66 REMARK 500 10 ARG A 27 28.18 38.73 REMARK 500 11 ARG A 4 -137.88 41.99 REMARK 500 11 LYS A 5 50.71 81.59 REMARK 500 11 CYS A 9 98.49 12.87 REMARK 500 11 CYS A 12 -65.82 -95.30 REMARK 500 11 ARG A 23 40.44 -90.56 REMARK 500 11 ARG A 27 23.87 49.37 REMARK 500 11 GLN A 28 33.69 -168.99 REMARK 500 12 ARG A 4 -164.42 37.08 REMARK 500 12 VAL A 6 171.14 -47.88 REMARK 500 12 CYS A 9 92.22 39.04 REMARK 500 12 CYS A 12 -61.31 -122.91 REMARK 500 12 ARG A 23 48.39 -82.76 REMARK 500 12 ARG A 26 75.17 -59.61 REMARK 500 13 GLN A 3 27.05 -171.41 REMARK 500 13 ARG A 4 72.51 21.18 REMARK 500 13 LYS A 5 61.26 -160.26 REMARK 500 13 CYS A 9 98.10 29.02 REMARK 500 13 TRP A 10 -19.02 -48.23 REMARK 500 13 CYS A 12 -67.60 -124.90 REMARK 500 13 ARG A 20 -39.82 -39.40 REMARK 500 13 CYS A 22 94.21 -56.94 REMARK 500 13 ALA A 24 167.43 -44.90 REMARK 500 13 ARG A 26 77.12 -59.18 REMARK 500 13 ARG A 27 26.21 44.49 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 ARG A 4 0.26 SIDE_CHAIN REMARK 500 1 ARG A 8 0.23 SIDE_CHAIN REMARK 500 1 ARG A 20 0.20 SIDE_CHAIN REMARK 500 1 ARG A 23 0.32 SIDE_CHAIN REMARK 500 1 ARG A 26 0.29 SIDE_CHAIN REMARK 500 1 ARG A 27 0.31 SIDE_CHAIN REMARK 500 2 ARG A 4 0.32 SIDE_CHAIN REMARK 500 2 ARG A 8 0.10 SIDE_CHAIN REMARK 500 2 ARG A 23 0.32 SIDE_CHAIN REMARK 500 2 ARG A 26 0.15 SIDE_CHAIN REMARK 500 2 ARG A 27 0.25 SIDE_CHAIN REMARK 500 3 ARG A 4 0.31 SIDE_CHAIN REMARK 500 3 ARG A 8 0.19 SIDE_CHAIN REMARK 500 3 ARG A 20 0.22 SIDE_CHAIN REMARK 500 3 ARG A 23 0.25 SIDE_CHAIN REMARK 500 3 ARG A 26 0.20 SIDE_CHAIN REMARK 500 3 ARG A 27 0.20 SIDE_CHAIN REMARK 500 4 ARG A 4 0.31 SIDE_CHAIN REMARK 500 4 ARG A 8 0.31 SIDE_CHAIN REMARK 500 4 ARG A 20 0.28 SIDE_CHAIN REMARK 500 4 ARG A 23 0.23 SIDE_CHAIN REMARK 500 4 ARG A 26 0.19 SIDE_CHAIN REMARK 500 4 ARG A 27 0.30 SIDE_CHAIN REMARK 500 5 ARG A 4 0.15 SIDE_CHAIN REMARK 500 5 ARG A 8 0.25 SIDE_CHAIN REMARK 500 5 ARG A 20 0.30 SIDE_CHAIN REMARK 500 5 ARG A 23 0.31 SIDE_CHAIN REMARK 500 5 ARG A 26 0.14 SIDE_CHAIN REMARK 500 5 ARG A 27 0.20 SIDE_CHAIN REMARK 500 6 ARG A 4 0.24 SIDE_CHAIN REMARK 500 6 ARG A 8 0.21 SIDE_CHAIN REMARK 500 6 ARG A 20 0.18 SIDE_CHAIN REMARK 500 6 ARG A 23 0.21 SIDE_CHAIN REMARK 500 6 ARG A 26 0.29 SIDE_CHAIN REMARK 500 6 ARG A 27 0.18 SIDE_CHAIN REMARK 500 7 ARG A 4 0.31 SIDE_CHAIN REMARK 500 7 ARG A 8 0.24 SIDE_CHAIN REMARK 500 7 ARG A 20 0.31 SIDE_CHAIN REMARK 500 7 ARG A 23 0.32 SIDE_CHAIN REMARK 500 7 ARG A 26 0.16 SIDE_CHAIN REMARK 500 7 ARG A 27 0.28 SIDE_CHAIN REMARK 500 8 ARG A 8 0.22 SIDE_CHAIN REMARK 500 8 ARG A 20 0.19 SIDE_CHAIN REMARK 500 8 ARG A 23 0.31 SIDE_CHAIN REMARK 500 8 ARG A 26 0.17 SIDE_CHAIN REMARK 500 8 ARG A 27 0.31 SIDE_CHAIN REMARK 500 9 ARG A 4 0.13 SIDE_CHAIN REMARK 500 9 ARG A 8 0.31 SIDE_CHAIN REMARK 500 9 ARG A 20 0.20 SIDE_CHAIN REMARK 500 9 ARG A 23 0.32 SIDE_CHAIN REMARK 500 9 ARG A 26 0.32 SIDE_CHAIN REMARK 500 9 ARG A 27 0.20 SIDE_CHAIN REMARK 500 10 ARG A 4 0.22 SIDE_CHAIN REMARK 500 10 ARG A 8 0.24 SIDE_CHAIN REMARK 500 10 ARG A 20 0.32 SIDE_CHAIN REMARK 500 10 ARG A 23 0.25 SIDE_CHAIN REMARK 500 10 ARG A 26 0.32 SIDE_CHAIN REMARK 500 10 ARG A 27 0.31 SIDE_CHAIN REMARK 500 11 ARG A 4 0.29 SIDE_CHAIN REMARK 500 11 ARG A 8 0.31 SIDE_CHAIN REMARK 500 11 ARG A 20 0.26 SIDE_CHAIN REMARK 500 11 ARG A 23 0.14 SIDE_CHAIN REMARK 500 11 ARG A 26 0.29 SIDE_CHAIN REMARK 500 11 ARG A 27 0.27 SIDE_CHAIN REMARK 500 12 ARG A 8 0.32 SIDE_CHAIN REMARK 500 12 ARG A 20 0.31 SIDE_CHAIN REMARK 500 12 ARG A 23 0.16 SIDE_CHAIN REMARK 500 12 ARG A 26 0.27 SIDE_CHAIN REMARK 500 12 ARG A 27 0.08 SIDE_CHAIN REMARK 500 13 ARG A 4 0.20 SIDE_CHAIN REMARK 500 13 ARG A 8 0.12 SIDE_CHAIN REMARK 500 13 ARG A 20 0.28 SIDE_CHAIN REMARK 500 13 ARG A 23 0.25 SIDE_CHAIN REMARK 500 13 ARG A 26 0.16 SIDE_CHAIN REMARK 500 13 ARG A 27 0.17 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 1 ZN A 30 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 76.7 REMARK 620 3 HIS A 17 NE2 102.4 144.5 REMARK 620 4 CYS A 22 SG 49.9 42.2 152.3 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 30
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NC8 RELATED DB: PDB REMARK 900 WILD TYPE SEQUENCE OF THE SAME PEPTIDE
DBREF 2DI2 A 1 29 UNP P18041 GAG_HV2G1 383 411
SEQADV 2DI2 ALA A 11 UNP P18041 ASN 393 ENGINEERED
SEQRES 1 A 29 ALA GLN GLN ARG LYS VAL ILE ARG CYS TRP ALA CYS GLY SEQRES 2 A 29 LYS GLU GLY HIS SER ALA ARG GLN CYS ARG ALA PRO ARG SEQRES 3 A 29 ARG GLN GLY
HET ZN A 30 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 SER A 18 CYS A 22 5 5
SSBOND 1 CYS A 9 CYS A 22 1555 1555 1.94 SSBOND 2 CYS A 12 CYS A 22 1555 1555 1.66
LINK ZN ZN A 30 SG CYS A 9 1555 1555 2.30 LINK ZN ZN A 30 SG CYS A 12 1555 1555 2.30 LINK ZN ZN A 30 NE2 HIS A 17 1555 1555 2.00 LINK ZN ZN A 30 SG CYS A 22 1555 1555 2.30
SITE 1 AC1 4 CYS A 9 CYS A 12 HIS A 17 CYS A 22
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