HEADER HYDROLASE/DNA 19-MAY-19 6K3K TITLE SOLUTION STRUCTURE OF APOBEC3G-CD2 WITH SSDNA, PRODUCT B COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3G; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APOBEC-RELATED CYTIDINE DEAMINASE,ARCD,APOBEC-RELATED COMPND 5 PROTEIN 9,ARP-9,CEM-15,CEM15,DEOXYCYTIDINE DEAMINASE,A3G; COMPND 6 EC: 3.5.4.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'); COMPND 10 CHAIN: B; COMPND 11 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: APOBEC3G; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS APOBEC3G, DNA CYTIDINE DEAMINASE COMPLEX WITH DNA, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.CAO,X.YAN,W.LAN,C.WANG REVDAT 3 14-JUN-23 6K3K 1 REMARK REVDAT 2 17-JUL-19 6K3K 1 JRNL REMARK REVDAT 1 12-JUN-19 6K3K 0 JRNL AUTH X.YAN,W.LAN,C.WANG,C.CAO JRNL TITL STRUCTURAL INVESTIGATIONS ON THE INTERACTIONS BETWEEN JRNL TITL 2 CYTIDINE DEAMINASE HUMAN APOBEC3G AND DNA. JRNL REF CHEM ASIAN J V. 14 2235 2019 JRNL REFN ESSN 1861-471X JRNL PMID 31116511 JRNL DOI 10.1002/ASIA.201900480 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6K3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300011683. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.35 MM [U-99% 13C; U-99% 15N] REMARK 210 DNA DC->DU-EDITING ENZYME APOBEC3G, 0.525 MM DNA/RNA (5'-D(*AP* REMARK 210 TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 5 MM DTT, 50 UM ZINC ION, 90% H2O/10% D2O; REMARK 210 0.35 MM [U-99% 13C; U-99% 15N] DNA DC->DU-EDITING ENZYME REMARK 210 APOBEC3G, 0.525 MM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP* REMARK 210 T)-3'), 50 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 5 MM DTT, REMARK 210 50 UM ZINC ION, 100% D2O; 0.35 MM [U-100% 13C; U-100% 15N; U-80% REMARK 210 2H] DNA DC->DU-EDITING ENZYME APOBEC3G, 0.525 MM DNA/RNA (5'-D(* REMARK 210 AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 5 MM DTT, 50 UM ZINC ION, 90% H2O/10% D2O; REMARK 210 1 MM DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3'), 50 REMARK 210 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 50 UM ZINC ION, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 2D 1H-15N HSQC; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N TOCSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-1H TOCSY; 2D REMARK 210 DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 850 MHZ; 900 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 O TRP A 211 H ARG A 213 1.57 REMARK 500 O ARG A 376 H GLN A 380 1.60 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 ASN A 207 21.69 -78.91 REMARK 500 1 TRP A 211 -9.15 -55.97 REMARK 500 1 VAL A 212 62.72 -66.82 REMARK 500 1 ARG A 320 -4.47 58.70 REMARK 500 1 ALA A 333 176.14 58.47 REMARK 500 1 ASP A 362 30.41 -91.52 REMARK 500 1 GLN A 382 97.83 -56.74 REMARK 500 2 ASN A 207 21.29 -77.35 REMARK 500 2 TRP A 211 -8.74 -58.73 REMARK 500 2 VAL A 212 66.01 -63.37 REMARK 500 2 ARG A 320 -12.60 61.81 REMARK 500 2 ALA A 333 176.24 59.11 REMARK 500 2 ASP A 362 30.22 -94.15 REMARK 500 2 GLN A 382 98.00 -59.97 REMARK 500 3 ASN A 207 23.10 -79.55 REMARK 500 3 TRP A 211 -8.39 -59.57 REMARK 500 3 VAL A 212 68.85 -63.20 REMARK 500 3 ARG A 320 -49.36 -176.43 REMARK 500 3 CYS A 321 27.72 -71.48 REMARK 500 3 ALA A 333 176.46 58.13 REMARK 500 3 ASP A 362 30.46 -90.67 REMARK 500 3 GLN A 382 97.90 -56.21 REMARK 500 4 TRP A 211 -9.45 -55.95 REMARK 500 4 VAL A 212 62.47 -68.51 REMARK 500 4 GLN A 237 39.15 -80.03 REMARK 500 4 ARG A 238 32.03 -92.91 REMARK 500 4 ARG A 320 -10.22 59.32 REMARK 500 4 CYS A 321 33.73 -81.89 REMARK 500 4 ALA A 333 176.76 58.47 REMARK 500 4 ASP A 352 92.64 -69.17 REMARK 500 4 ASP A 362 30.89 -87.30 REMARK 500 4 GLN A 382 98.03 -52.78 REMARK 500 5 PRO A 199 153.89 -33.70 REMARK 500 5 PRO A 200 69.94 -23.83 REMARK 500 5 ASN A 208 29.67 -66.71 REMARK 500 5 TRP A 211 -9.88 -59.15 REMARK 500 5 VAL A 212 62.30 -69.00 REMARK 500 5 ARG A 320 9.89 47.30 REMARK 500 5 CYS A 321 30.40 -96.88 REMARK 500 5 ALA A 333 176.76 58.26 REMARK 500 5 ASP A 362 30.24 -91.81 REMARK 500 5 GLN A 382 97.64 -56.70 REMARK 500 6 TRP A 211 -9.67 -56.02 REMARK 500 6 VAL A 212 62.53 -66.50 REMARK 500 6 ARG A 320 2.93 54.23 REMARK 500 6 ALA A 333 176.40 58.39 REMARK 500 6 ASP A 362 30.86 -88.29 REMARK 500 6 GLN A 382 97.83 -48.39 REMARK 500 7 TRP A 211 -9.42 -57.08 REMARK 500 7 VAL A 212 64.51 -66.06 REMARK 500 REMARK 500 THIS ENTRY HAS 148 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 257 ND1 REMARK 620 2 CYS A 288 SG 114.8 REMARK 620 3 CYS A 291 SG 111.8 107.7 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 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36193 RELATED DB: BMRB DBREF 6K3K A 197 384 UNP Q9HC16 ABC3G_HUMAN 197 384 DBREF 6K3K B 385 394 PDB 6K3K 6K3K 385 394 SEQRES 1 A 188 MET ASP PRO PRO THR PHE THR PHE ASN PHE ASN ASN GLU SEQRES 2 A 188 PRO TRP VAL ARG GLY ARG HIS GLU THR TYR LEU CYS TYR SEQRES 3 A 188 GLU VAL GLU ARG MET HIS ASN ASP THR TRP VAL LEU LEU SEQRES 4 A 188 ASN GLN ARG ARG GLY PHE LEU CYS ASN GLN ALA PRO HIS SEQRES 5 A 188 LYS HIS GLY PHE LEU GLU GLY ARG HIS ALA GLU LEU CYS SEQRES 6 A 188 PHE LEU ASP VAL ILE PRO PHE TRP LYS LEU ASP LEU ASP SEQRES 7 A 188 GLN ASP TYR ARG VAL THR CYS PHE THR SER TRP SER PRO SEQRES 8 A 188 CYS PHE SER CYS ALA GLN GLU MET ALA LYS PHE ILE SER SEQRES 9 A 188 LYS ASN LYS HIS VAL SER LEU CYS ILE PHE THR ALA ARG SEQRES 10 A 188 ILE TYR ASP ASP GLN GLY ARG CYS GLN GLU GLY LEU ARG SEQRES 11 A 188 THR LEU ALA GLU ALA GLY ALA LYS ILE SER ILE MET THR SEQRES 12 A 188 TYR SER GLU PHE LYS HIS CYS TRP ASP THR PHE VAL ASP SEQRES 13 A 188 HIS GLN GLY CYS PRO PHE GLN PRO TRP ASP GLY LEU ASP SEQRES 14 A 188 GLU HIS SER GLN ASP LEU SER GLY ARG LEU ARG ALA ILE SEQRES 15 A 188 LEU GLN ASN GLN GLU ASN SEQRES 1 B 10 DA DT DT DC DU C38 DA DA DT DT HET C38 B 390 30 HET ZN A 401 1 HETNAM C38 5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 C38 C9 H13 I N3 O7 P FORMUL 3 ZN ZN 2+ HELIX 1 AA1 PRO A 200 ASN A 207 1 8 HELIX 2 AA2 ASN A 208 VAL A 212 5 5 HELIX 3 AA3 LEU A 234 ARG A 238 5 5 HELIX 4 AA4 HIS A 257 TRP A 269 1 13 HELIX 5 AA5 CYS A 288 ASN A 302 1 15 HELIX 6 AA6 CYS A 321 GLY A 332 1 12 HELIX 7 AA7 THR A 339 VAL A 351 1 13 HELIX 8 AA8 ASP A 362 ASN A 381 1 20 SHEET 1 AA1 3 TRP A 232 VAL A 233 0 SHEET 2 AA1 3 LEU A 220 MET A 227 -1 N ARG A 226 O VAL A 233 SHEET 3 AA1 3 GLY A 240 LEU A 242 -1 O LEU A 242 N LEU A 220 SHEET 1 AA2 5 TRP A 232 VAL A 233 0 SHEET 2 AA2 5 LEU A 220 MET A 227 -1 N ARG A 226 O VAL A 233 SHEET 3 AA2 5 ASP A 276 THR A 283 -1 O PHE A 282 N CYS A 221 SHEET 4 AA2 5 VAL A 305 THR A 311 1 O SER A 306 N TYR A 277 SHEET 5 AA2 5 LYS A 334 ILE A 337 1 O LYS A 334 N ILE A 309 LINK O3' DU B 389 P C38 B 390 1555 1555 1.61 LINK O3' C38 B 390 P DA B 391 1555 1555 1.60 LINK ND1 HIS A 257 ZN ZN A 401 1555 1555 2.01 LINK SG CYS A 288 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 291 ZN ZN A 401 1555 1555 2.30 SITE 1 AC1 3 HIS A 257 CYS A 288 CYS A 291 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