HEADER HYDROLASE/DNA 19-MAY-19 6K3J TITLE SOLUTION STRUCTURE OF APOBEC3G-CD2 WITH SSDNA, PRODUCT A 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 (5'-D(*AP*TP*TP*CP*UP*(IUR)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 4 15-MAY-24 6K3J 1 REMARK REVDAT 3 14-JUN-23 6K3J 1 REMARK REVDAT 2 17-JUL-19 6K3J 1 JRNL REMARK REVDAT 1 12-JUN-19 6K3J 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 6K3J 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_1300012220. 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 (5'-D(*AP*TP*TP* REMARK 210 CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 5 MM DTT, 50 UM ZINC ION, 90% H2O/10% D2O; 0.35 REMARK 210 MM [U-99% 13C; U-99% 15N] DNA DC->DU-EDITING ENZYME APOBEC3G, REMARK 210 0.525 MM DNA (5'-D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 5 MM DTT, 50 UM ZINC REMARK 210 ION, 100% D2O; 0.35 MM [U-100% 13C; U-100% 15N; U-80% 2H] DNA DC- REMARK 210 >DU-EDITING ENZYME APOBEC3G, 0.525 MM DNA (5'-D(*AP*TP*TP*CP*UP* REMARK 210 (IUR)P*AP*AP*TP*T)-3'), 50 MM SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 50 UM ZINC ION, 90% H2O/10% D2O; 1 MM DNA (5' REMARK 210 -D(*AP*TP*TP*CP*UP*(IUR)P*AP*AP*TP*T)-3'), 50 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, 90% 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; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D 1H-15N NOESY; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N TOCSY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 2D DQF-COSY; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY 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 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 13 DT B 386 C6 - C5 - C7 ANGL. DEV. = -3.6 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 PRO A 199 156.33 -36.52 REMARK 500 1 PRO A 200 69.67 -41.09 REMARK 500 1 ASN A 208 28.55 -69.45 REMARK 500 1 VAL A 212 76.37 -56.96 REMARK 500 1 SER A 284 53.85 -119.32 REMARK 500 1 CYS A 288 -157.80 83.35 REMARK 500 1 PHE A 289 -68.93 -137.48 REMARK 500 1 ARG A 320 -36.02 -176.75 REMARK 500 1 ALA A 333 177.21 58.55 REMARK 500 1 ASP A 362 30.93 -76.08 REMARK 500 1 GLN A 382 98.49 -49.67 REMARK 500 2 PRO A 199 156.36 -36.48 REMARK 500 2 PRO A 200 63.65 -40.96 REMARK 500 2 ASN A 244 11.36 -67.01 REMARK 500 2 LYS A 270 64.16 39.94 REMARK 500 2 SER A 284 52.16 -110.11 REMARK 500 2 ARG A 320 1.87 54.69 REMARK 500 2 ALA A 333 177.55 58.62 REMARK 500 2 ASP A 362 30.55 -84.17 REMARK 500 2 GLN A 382 98.73 -59.24 REMARK 500 3 PRO A 199 156.41 -35.50 REMARK 500 3 PRO A 200 69.61 -41.86 REMARK 500 3 ASN A 244 2.53 -69.23 REMARK 500 3 SER A 284 52.37 -113.53 REMARK 500 3 ARG A 320 -42.41 -175.50 REMARK 500 3 CYS A 321 37.39 -68.83 REMARK 500 3 ALA A 333 176.18 59.63 REMARK 500 3 GLN A 354 111.22 -5.78 REMARK 500 3 ASP A 362 29.99 -75.94 REMARK 500 3 GLN A 382 97.56 -55.12 REMARK 500 4 PRO A 199 154.53 -35.11 REMARK 500 4 PRO A 200 69.54 -40.88 REMARK 500 4 VAL A 212 77.32 -56.50 REMARK 500 4 SER A 284 52.15 -109.13 REMARK 500 4 ARG A 320 3.03 54.49 REMARK 500 4 ALA A 333 176.14 58.04 REMARK 500 4 GLN A 354 111.40 -5.52 REMARK 500 4 ASP A 362 30.33 -81.66 REMARK 500 4 GLN A 382 98.59 -57.03 REMARK 500 5 PRO A 199 156.20 -36.58 REMARK 500 5 PRO A 200 63.34 -40.08 REMARK 500 5 ASN A 208 24.39 -78.10 REMARK 500 5 VAL A 212 109.86 -59.79 REMARK 500 5 GLN A 237 71.16 -58.35 REMARK 500 5 ASN A 244 11.31 -67.24 REMARK 500 5 GLN A 318 83.37 -172.54 REMARK 500 5 ALA A 333 176.64 56.89 REMARK 500 5 ASP A 362 29.47 -76.31 REMARK 500 5 GLN A 382 98.54 -51.72 REMARK 500 6 PRO A 199 156.45 -35.40 REMARK 500 REMARK 500 THIS ENTRY HAS 180 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 110.9 REMARK 620 3 CYS A 291 SG 105.5 111.5 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 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36193 RELATED DB: BMRB DBREF 6K3J A 197 384 UNP Q9HC16 ABC3G_HUMAN 197 384 DBREF 6K3J B 385 394 PDB 6K3J 6K3J 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 5IU DA DA DT DT HET 5IU B 390 29 HET ZN A 401 1 HETNAM 5IU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 5IU C9 H12 I N2 O8 P FORMUL 3 ZN ZN 2+ HELIX 1 AA1 PRO A 200 ASN A 207 1 8 HELIX 2 AA2 LEU A 234 ARG A 238 5 5 HELIX 3 AA3 PRO A 247 GLY A 251 5 5 HELIX 4 AA4 HIS A 257 TRP A 269 1 13 HELIX 5 AA5 PHE A 289 ASN A 302 1 14 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 TYR A 219 MET A 227 -1 N ARG A 226 O VAL A 233 SHEET 3 AA1 3 GLY A 240 CYS A 243 -1 O LEU A 242 N LEU A 220 SHEET 1 AA2 5 TRP A 232 VAL A 233 0 SHEET 2 AA2 5 TYR A 219 MET A 227 -1 N ARG A 226 O VAL A 233 SHEET 3 AA2 5 ASP A 276 THR A 283 -1 O ASP A 276 N MET A 227 SHEET 4 AA2 5 VAL A 305 THR A 311 1 O PHE A 310 N CYS A 281 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 5IU B 390 1555 1555 1.61 LINK O3' 5IU B 390 P DA B 391 1555 1555 1.61 LINK ND1 HIS A 257 ZN ZN A 401 1555 1555 2.00 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