PDB Short entry for 2KBO HEADER HYDROLASE 04-DEC-08 2KBO TITLE STRUCTURE, INTERACTION, AND REAL-TIME MONITORING OF THE ENZYMATIC TITLE 2 REACTION OF WILD TYPE APOBEC3G COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3G; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 193-384; COMPND 5 SYNONYM: APOBEC-RELATED CYTIDINE DEAMINASE, ARCD, APOBEC-RELATED COMPND 6 PROTEIN, ARP-9, CEM-15, CEM15; COMPND 7 EC: 3.5.4.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MDS019; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15(B) KEYWDS CYTIDINE DEAMINASE, HIV, APOBEC3G, ALTERNATIVE SPLICING, ANTIVIRAL KEYWDS 2 DEFENSE, CYTOPLASM, HOST-VIRUS INTERACTION, HYDROLASE, METAL- KEYWDS 3 BINDING, NUCLEUS, POLYMORPHISM, UBL CONJUGATION, ZINC EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.FURUKAWA,T.NAGATA,A.MATSUGAMI,Y.HABU,R.SUGIYAMA,F.HAYASHI, AUTHOR 2 N.KOBAYASHI,S.YOKOYAMA,H.TAKAKU,M.KATAHIRA REVDAT 3 16-MAR-22 2KBO 1 REMARK SEQADV REVDAT 2 07-APR-09 2KBO 1 JRNL REVDAT 1 03-FEB-09 2KBO 0 JRNL AUTH A.FURUKAWA,T.NAGATA,A.MATSUGAMI,Y.HABU,R.SUGIYAMA,F.HAYASHI, JRNL AUTH 2 N.KOBAYASHI,S.YOKOYAMA,H.TAKAKU,M.KATAHIRA JRNL TITL STRUCTURE, INTERACTION AND REAL-TIME MONITORING OF THE JRNL TITL 2 ENZYMATIC REACTION OF WILD-TYPE APOBEC3G JRNL REF EMBO J. V. 28 440 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19153609 JRNL DOI 10.1038/EMBOJ.2008.290 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 97.027.12.56, X-PLOR NIH 2.20 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000100920. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 30 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3MM [U-100% 13C; U-100% 15N] REMARK 210 APOBEC3G-1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 3D CBCA(CO)NH; 3D C(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW 2.4, XWINNMR 3.5, KUJIRA REMARK 210 0.9820, X-PLOR NIH 2.20 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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: 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 HH11 ARG A 4 HG SER A 6 0.81 REMARK 500 HE22 GLN A 47 NH2 ARG A 49 0.90 REMARK 500 NH1 ARG A 4 OG SER A 6 0.92 REMARK 500 HE22 GLN A 47 HH22 ARG A 49 0.93 REMARK 500 NH1 ARG A 4 HG SER A 6 1.03 REMARK 500 HH12 ARG A 4 CB SER A 6 1.09 REMARK 500 HH12 ARG A 4 HB2 SER A 6 1.12 REMARK 500 HG CYS A 71 H PHE A 72 1.22 REMARK 500 NE2 GLN A 47 HH22 ARG A 49 1.23 REMARK 500 HG CYS A 166 H PHE A 168 1.31 REMARK 500 CZ ARG A 4 OG SER A 6 1.32 REMARK 500 HE21 GLN A 47 HH22 ARG A 49 1.32 REMARK 500 HE22 GLN A 132 HH11 ARG A 184 1.33 REMARK 500 HH12 ARG A 4 OG SER A 6 1.43 REMARK 500 O VAL A 75 H PHE A 78 1.49 REMARK 500 HH11 ARG A 4 OG SER A 6 1.50 REMARK 500 O ALA A 106 H SER A 110 1.55 REMARK 500 NH1 ARG A 4 CB SER A 6 1.59 REMARK 500 NE2 GLN A 47 NH2 ARG A 49 1.80 REMARK 500 O ALA A 68 SG CYS A 71 1.89 REMARK 500 O CYS A 156 CE1 PHE A 160 2.05 REMARK 500 O CYS A 156 CZ PHE A 160 2.08 REMARK 500 NH2 ARG A 4 OG SER A 6 2.15 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 LEU A 3 -100.40 -89.78 REMARK 500 1 SER A 6 87.95 -57.32 REMARK 500 1 MET A 7 126.96 -39.49 REMARK 500 1 ASP A 8 -46.71 167.01 REMARK 500 1 ASN A 15 -133.92 -147.74 REMARK 500 1 ASN A 17 23.63 48.57 REMARK 500 1 ASN A 18 -13.37 -47.40 REMARK 500 1 GLU A 19 89.45 -22.75 REMARK 500 1 PRO A 20 -170.47 -49.52 REMARK 500 1 VAL A 22 168.30 -46.66 REMARK 500 1 ARG A 23 53.83 36.87 REMARK 500 1 ARG A 25 21.60 -166.03 REMARK 500 1 HIS A 26 -49.57 -140.21 REMARK 500 1 THR A 28 -173.37 -59.84 REMARK 500 1 TYR A 29 125.16 173.36 REMARK 500 1 ASN A 39 -158.12 65.96 REMARK 500 1 ASP A 40 9.87 -56.20 REMARK 500 1 ARG A 48 -86.00 -91.07 REMARK 500 1 ASN A 54 146.80 56.79 REMARK 500 1 LYS A 59 100.49 54.77 REMARK 500 1 ALA A 68 -49.15 -26.41 REMARK 500 1 LEU A 81 -144.27 -63.38 REMARK 500 1 ASP A 82 -165.79 -119.73 REMARK 500 1 SER A 94 -11.99 -44.80 REMARK 500 1 PRO A 97 -151.78 -81.80 REMARK 500 1 CYS A 101 -28.73 -38.23 REMARK 500 1 MET A 105 -71.62 -57.25 REMARK 500 1 LYS A 107 -71.05 -48.76 REMARK 500 1 PHE A 108 -33.32 -35.85 REMARK 500 1 ILE A 109 -71.08 -84.71 REMARK 500 1 HIS A 114 -12.54 -43.29 REMARK 500 1 ALA A 122 -65.78 -95.19 REMARK 500 1 GLN A 128 -107.68 -98.39 REMARK 500 1 GLN A 132 -10.53 -49.45 REMARK 500 1 MET A 148 98.75 -68.61 REMARK 500 1 PHE A 153 -75.26 -74.08 REMARK 500 1 ASP A 158 -5.57 -52.01 REMARK 500 1 ASP A 162 39.77 -70.56 REMARK 500 1 HIS A 163 89.22 -163.09 REMARK 500 1 GLN A 164 -7.74 -48.83 REMARK 500 1 CYS A 166 165.42 -44.41 REMARK 500 1 ASP A 172 42.82 -68.71 REMARK 500 1 LEU A 174 -26.02 -37.29 REMARK 500 1 ARG A 184 -70.58 -77.21 REMARK 500 1 GLN A 190 16.95 -66.58 REMARK 500 1 ASN A 191 57.20 25.63 REMARK 500 1 GLN A 192 104.49 -47.72 REMARK 500 1 GLU A 193 -179.57 -47.01 REMARK 500 2 ARG A 4 131.51 62.57 REMARK 500 2 SER A 6 -108.02 -104.55 REMARK 500 REMARK 500 THIS ENTRY HAS 455 RAMACHANDRAN OUTLIERS. 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 250 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 ND1 REMARK 620 2 CYS A 98 SG 109.9 REMARK 620 3 CYS A 101 SG 111.4 108.5 REMARK 620 N 1 2 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 250 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JYW RELATED DB: PDB REMARK 900 RELATED ID: 3E1U RELATED DB: PDB DBREF 2KBO A 3 194 UNP Q9HC16 ABC3G_HUMAN 193 384 SEQADV 2KBO HIS A 1 UNP Q9HC16 EXPRESSION TAG SEQADV 2KBO MET A 2 UNP Q9HC16 EXPRESSION TAG SEQRES 1 A 194 HIS MET LEU ARG HIS SER MET ASP PRO PRO THR PHE THR SEQRES 2 A 194 PHE ASN PHE ASN ASN GLU PRO TRP VAL ARG GLY ARG HIS SEQRES 3 A 194 GLU THR TYR LEU CYS TYR GLU VAL GLU ARG MET HIS ASN SEQRES 4 A 194 ASP THR TRP VAL LEU LEU ASN GLN ARG ARG GLY PHE LEU SEQRES 5 A 194 CYS ASN GLN ALA PRO HIS LYS HIS GLY PHE LEU GLU GLY SEQRES 6 A 194 ARG HIS ALA GLU LEU CYS PHE LEU ASP VAL ILE PRO PHE SEQRES 7 A 194 TRP LYS LEU ASP LEU ASP GLN ASP TYR ARG VAL THR CYS SEQRES 8 A 194 PHE THR SER TRP SER PRO CYS PHE SER CYS ALA GLN GLU SEQRES 9 A 194 MET ALA LYS PHE ILE SER LYS ASN LYS HIS VAL SER LEU SEQRES 10 A 194 CYS ILE PHE THR ALA ARG ILE TYR ASP ASP GLN GLY ARG SEQRES 11 A 194 CYS GLN GLU GLY LEU ARG THR LEU ALA GLU ALA GLY ALA SEQRES 12 A 194 LYS ILE SER ILE MET THR TYR SER GLU PHE LYS HIS CYS SEQRES 13 A 194 TRP ASP THR PHE VAL ASP HIS GLN GLY CYS PRO PHE GLN SEQRES 14 A 194 PRO TRP ASP GLY LEU ASP GLU HIS SER GLN ASP LEU SER SEQRES 15 A 194 GLY ARG LEU ARG ALA ILE LEU GLN ASN GLN GLU ASN HET ZN A 250 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 8 ASN A 15 1 8 HELIX 2 2 HIS A 67 LYS A 80 1 14 HELIX 3 3 CYS A 98 LYS A 111 1 14 HELIX 4 4 GLY A 129 CYS A 131 5 3 HELIX 5 5 GLN A 132 GLY A 142 1 11 HELIX 6 6 THR A 149 VAL A 161 1 13 HELIX 7 7 GLY A 173 GLN A 190 1 18 SHEET 1 A 5 THR A 41 TRP A 42 0 SHEET 2 A 5 CYS A 31 HIS A 38 -1 N HIS A 38 O THR A 41 SHEET 3 A 5 ASP A 86 PHE A 92 -1 O THR A 90 N GLU A 33 SHEET 4 A 5 VAL A 115 THR A 121 1 O PHE A 120 N CYS A 91 SHEET 5 A 5 ALA A 143 ILE A 147 1 O LYS A 144 N LEU A 117 LINK ND1 HIS A 67 ZN ZN A 250 1555 1555 2.02 LINK SG CYS A 98 ZN ZN A 250 1555 1555 2.30 LINK SG CYS A 101 ZN ZN A 250 1555 1555 2.29 SITE 1 AC1 3 ARG A 23 GLY A 65 TRP A 95 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