HEADER VIRAL PROTEIN 30-MAR-90 2ZNF TITLE HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW TITLE 2 NMR-BASED DISTANCE GEOMETRY APPROACH COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676 KEYWDS AIDS-RELATED VIRUS GAG POLYPROTEIN, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR M.F.SUMMERS,T.L.SOUTH,B.KIM,D.R.HARE REVDAT 4 23-MAR-22 2ZNF 1 REMARK LINK REVDAT 3 24-FEB-09 2ZNF 1 VERSN REVDAT 2 15-JUL-92 2ZNF 1 FORMUL REVDAT 1 15-OCT-91 2ZNF 0 JRNL AUTH M.F.SUMMERS,T.L.SOUTH,B.KIM,D.R.HARE JRNL TITL HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN JRNL TITL 2 VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH. JRNL REF BIOCHEMISTRY V. 29 329 1990 JRNL REFN ISSN 0006-2960 JRNL PMID 2105740 JRNL DOI 10.1021/BI00454A005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZNF 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_1000178766. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: 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 2 GLU A 9 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 5 GLU A 9 CA - CB - CG ANGL. DEV. = 13.6 DEGREES REMARK 500 9 GLU A 9 CA - CB - CG ANGL. DEV. = 16.5 DEGREES REMARK 500 10 CYS A 16 CB - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 15 GLU A 9 CA - CB - CG ANGL. DEV. = 17.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 2 146.09 85.30 REMARK 500 1 ASN A 15 28.78 -141.29 REMARK 500 1 CYS A 16 145.22 -27.72 REMARK 500 1 ARG A 17 46.55 -104.04 REMARK 500 2 ASN A 15 29.79 -140.68 REMARK 500 2 CYS A 16 146.92 -32.13 REMARK 500 3 LYS A 2 146.28 76.26 REMARK 500 3 ASN A 15 30.41 -142.29 REMARK 500 3 CYS A 16 148.38 -32.15 REMARK 500 4 LYS A 2 102.21 -53.26 REMARK 500 4 CYS A 3 96.25 -48.18 REMARK 500 4 PHE A 4 -32.47 -33.58 REMARK 500 4 ASN A 15 30.23 -140.91 REMARK 500 4 CYS A 16 146.62 -32.13 REMARK 500 5 CYS A 3 95.78 -67.14 REMARK 500 5 PHE A 4 -32.32 -33.58 REMARK 500 5 CYS A 16 155.99 -38.16 REMARK 500 6 LYS A 2 100.54 170.29 REMARK 500 6 CYS A 3 95.39 -44.94 REMARK 500 6 PHE A 4 -34.53 -31.41 REMARK 500 6 GLU A 9 122.96 -38.51 REMARK 500 6 CYS A 16 134.46 -29.54 REMARK 500 7 LYS A 2 126.10 -175.21 REMARK 500 7 PHE A 4 -36.82 -34.05 REMARK 500 7 ASN A 15 32.17 -143.83 REMARK 500 7 CYS A 16 -51.92 -29.78 REMARK 500 7 ARG A 17 79.74 70.78 REMARK 500 8 LYS A 2 138.20 68.06 REMARK 500 8 CYS A 16 148.76 -31.47 REMARK 500 9 LYS A 2 108.51 81.84 REMARK 500 9 GLU A 9 89.92 -39.89 REMARK 500 9 ASN A 15 27.12 -141.31 REMARK 500 9 CYS A 16 147.91 -24.70 REMARK 500 10 LYS A 2 90.07 39.80 REMARK 500 10 GLU A 9 96.44 -54.86 REMARK 500 10 ASN A 15 32.63 -143.64 REMARK 500 10 CYS A 16 -97.32 -22.73 REMARK 500 10 ARG A 17 -4.31 160.85 REMARK 500 11 LYS A 2 148.50 -173.93 REMARK 500 11 GLU A 9 90.99 -40.22 REMARK 500 11 CYS A 16 -67.07 -29.58 REMARK 500 11 ARG A 17 72.21 83.06 REMARK 500 12 GLU A 9 89.97 -51.27 REMARK 500 12 CYS A 16 137.74 -27.15 REMARK 500 13 LYS A 2 154.56 173.85 REMARK 500 13 GLU A 9 80.97 -51.54 REMARK 500 13 ASN A 15 30.88 -147.69 REMARK 500 13 CYS A 16 147.92 -26.79 REMARK 500 14 LYS A 2 144.55 -178.18 REMARK 500 14 CYS A 16 -76.06 -28.93 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 13 ARG A 14 1 -142.86 REMARK 500 ALA A 13 ARG A 14 2 -144.61 REMARK 500 GLY A 10 HIS A 11 3 -149.69 REMARK 500 ALA A 13 ARG A 14 3 -144.57 REMARK 500 ALA A 13 ARG A 14 4 -144.89 REMARK 500 ALA A 13 ARG A 14 5 -145.55 REMARK 500 ASN A 15 CYS A 16 5 149.13 REMARK 500 ALA A 13 ARG A 14 6 -142.96 REMARK 500 ALA A 13 ARG A 14 7 -143.26 REMARK 500 GLY A 10 HIS A 11 8 -149.12 REMARK 500 ALA A 13 ARG A 14 8 -144.99 REMARK 500 ALA A 13 ARG A 14 9 -143.75 REMARK 500 GLY A 10 HIS A 11 10 -149.52 REMARK 500 ALA A 13 ARG A 14 10 -144.66 REMARK 500 GLY A 10 HIS A 11 11 -149.38 REMARK 500 ALA A 13 ARG A 14 11 -144.90 REMARK 500 ALA A 13 ARG A 14 12 -143.87 REMARK 500 GLY A 10 HIS A 11 13 -149.02 REMARK 500 ALA A 13 ARG A 14 13 -144.05 REMARK 500 ALA A 13 ARG A 14 14 -142.91 REMARK 500 ALA A 13 ARG A 14 15 -146.69 REMARK 500 ASN A 15 CYS A 16 15 149.53 REMARK 500 ALA A 13 ARG A 14 16 -145.30 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 HIS A 11 0.10 SIDE CHAIN REMARK 500 2 HIS A 11 0.10 SIDE CHAIN REMARK 500 3 HIS A 11 0.09 SIDE CHAIN REMARK 500 4 HIS A 11 0.10 SIDE CHAIN REMARK 500 5 HIS A 11 0.09 SIDE CHAIN REMARK 500 7 HIS A 11 0.09 SIDE CHAIN REMARK 500 8 HIS A 11 0.10 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 ZN A 19 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 CYS A 6 SG 106.0 REMARK 620 3 HIS A 11 NE2 97.4 114.5 REMARK 620 4 CYS A 16 SG 111.3 114.2 111.9 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 19 DBREF 2ZNF A 1 18 UNP Q70622 GAG_HV1LW 389 406 SEQRES 1 A 18 VAL LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS ILE ALA SEQRES 2 A 18 ARG ASN CYS ARG ALA HET ZN A 19 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ LINK SG CYS A 3 ZN ZN A 19 1555 1555 2.32 LINK SG CYS A 6 ZN ZN A 19 1555 1555 2.29 LINK NE2 HIS A 11 ZN ZN A 19 1555 1555 2.03 LINK SG CYS A 16 ZN ZN A 19 1555 1555 2.30 SITE 1 AC1 4 CYS A 3 CYS A 6 HIS A 11 CYS A 16 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