HEADER HYDROLASE/DNA 11-DEC-17 6BUX TITLE CRYSTAL STRUCTURE OF APOBEC3G CATALYTIC DOMAIN COMPLEX WITH SUBSTRATE TITLE 2 SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN B MRNA EDITING ENZYME CATALYTIC SUBUNIT 3G COMPND 3 CATALYTIC DOMAIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*AP*AP*TP*CP*CP*CP*AP*AP*A)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, ANTIVIRAL DEFENCE, DNA CYTIDINE DEAMINASE, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MAITI,H.MATSUO REVDAT 3 04-OCT-23 6BUX 1 REMARK REVDAT 2 01-JAN-20 6BUX 1 REMARK REVDAT 1 18-JUL-18 6BUX 0 JRNL AUTH A.MAITI,W.MYINT,T.KANAI,K.DELVIKS-FRANKENBERRY, JRNL AUTH 2 C.SIERRA RODRIGUEZ,V.K.PATHAK,C.A.SCHIFFER,H.MATSUO JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HIV-1 JRNL TITL 2 RESTRICTION FACTOR APOBEC3G IN COMPLEX WITH SSDNA. JRNL REF NAT COMMUN V. 9 2460 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29941968 JRNL DOI 10.1038/S41467-018-04872-8 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.6163 - 3.5504 1.00 2640 137 0.1589 0.1714 REMARK 3 2 3.5504 - 2.8183 1.00 2575 137 0.1834 0.2292 REMARK 3 3 2.8183 - 2.4621 1.00 2555 125 0.2049 0.2322 REMARK 3 4 2.4621 - 2.2370 1.00 2578 118 0.1956 0.2548 REMARK 3 5 2.2370 - 2.0767 1.00 2537 153 0.1874 0.2493 REMARK 3 6 2.0767 - 1.9543 1.00 2529 154 0.1891 0.2259 REMARK 3 7 1.9543 - 1.8564 0.98 2471 134 0.1918 0.2323 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1805 REMARK 3 ANGLE : 0.762 2476 REMARK 3 CHIRALITY : 0.050 255 REMARK 3 PLANARITY : 0.006 291 REMARK 3 DIHEDRAL : 12.825 1391 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1000231656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18860 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.856 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 24.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32800 REMARK 200 FOR SHELL : 6.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3IR2 (CHAIN A) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG6000, 50 MM DI-SODIUM L-MALATE; REMARK 280 PH5.0, 30 MM CACL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.61850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 186 REMARK 465 PRO A 187 REMARK 465 LEU A 188 REMARK 465 GLY A 189 REMARK 465 SER A 190 REMARK 465 GLU A 191 REMARK 465 ILE A 192 REMARK 465 LEU A 193 REMARK 465 ASN A 384 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 229 CG OD1 ND2 REMARK 470 HIS A 250 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 273 CG CD1 CD2 REMARK 470 LYS A 334 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B -1 O3' DC B -1 C3' -0.039 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 ARG A 238 59.04 -104.44 REMARK 500 PHE A 252 55.05 -159.08 REMARK 500 LEU A 273 0.96 -66.61 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 112.7 REMARK 620 3 CYS A 291 SG 116.2 116.6 REMARK 620 4 HOH B 110 O 104.9 109.8 94.1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 DBREF 6BUX A 186 384 PDB 6BUX 6BUX 186 384 DBREF 6BUX B -5 3 PDB 6BUX 6BUX -5 3 SEQRES 1 A 199 GLY PRO LEU GLY SER GLU ILE LEU ARG HIS SER MET ASP SEQRES 2 A 199 PRO ALA THR PHE THR PHE ASN PHE ASN ASN GLU PRO TRP SEQRES 3 A 199 VAL ARG GLY ARG HIS GLU THR TYR LEU CYS TYR GLU VAL SEQRES 4 A 199 GLU ARG MET HIS ASN ASP THR TRP VAL LYS LEU ALA GLN SEQRES 5 A 199 ARG ARG GLY PHE LEU ALA ASN GLN ALA LYS HIS LYS HIS SEQRES 6 A 199 GLY PHE LEU GLU GLY ARG HIS ALA ALA LEU CYS PHE LEU SEQRES 7 A 199 ASP VAL ILE PRO PHE TRP LYS LEU ASP LEU ASP GLN ASP SEQRES 8 A 199 TYR ARG VAL THR CYS PHE THR SER TRP SER PRO CYS PHE SEQRES 9 A 199 SER CYS ALA GLN GLU MET ALA LYS PHE ILE SER LYS ASN SEQRES 10 A 199 LYS HIS VAL SER LEU CYS ILE LYS THR ALA ARG ILE TYR SEQRES 11 A 199 ASP ASP LYS GLY ARG ALA ALA GLU GLY LEU ARG THR LEU SEQRES 12 A 199 ALA GLU ALA GLY ALA LYS ILE SER ILE MET THR TYR SER SEQRES 13 A 199 GLU PHE LYS HIS CYS TRP ASP THR PHE VAL ASP HIS GLN SEQRES 14 A 199 GLY ALA PRO PHE GLN PRO TRP ASP GLY LEU ASP GLU HIS SEQRES 15 A 199 SER GLN ASP LEU SER GLY ARG LEU ARG ALA ILE LEU GLN SEQRES 16 A 199 ASN GLN GLU ASN SEQRES 1 B 9 DA DA DT DC DC DC DA DA DA HET ZN A 401 1 HET GOL A 402 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN ZN 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *154(H2 O) HELIX 1 AA1 ASP A 198 ASN A 207 1 10 HELIX 2 AA2 HIS A 257 LYS A 270 1 14 HELIX 3 AA3 CYS A 288 ASN A 302 1 15 HELIX 4 AA4 ARG A 320 ALA A 331 1 12 HELIX 5 AA5 THR A 339 VAL A 351 1 13 HELIX 6 AA6 GLY A 363 GLN A 380 1 18 SHEET 1 AA1 6 THR A 231 LYS A 234 0 SHEET 2 AA1 6 GLY A 240 ALA A 243 1 SHEET 3 AA1 6 TYR A 219 HIS A 228 -1 N TYR A 222 O GLY A 240 SHEET 4 AA1 6 TYR A 277 TRP A 285 -1 O PHE A 282 N CYS A 221 SHEET 5 AA1 6 VAL A 305 ARG A 313 1 O LYS A 310 N CYS A 281 SHEET 6 AA1 6 LYS A 334 ILE A 337 1 O LYS A 334 N ILE A 309 LINK ND1 HIS A 257 ZN ZN A 401 1555 1555 2.09 LINK SG CYS A 288 ZN ZN A 401 1555 1555 2.25 LINK SG CYS A 291 ZN ZN A 401 1555 1555 2.17 LINK ZN ZN A 401 O HOH B 110 1555 1555 2.35 SITE 1 AC1 4 HIS A 257 CYS A 288 CYS A 291 HOH B 110 SITE 1 AC2 2 PHE A 204 HOH A 502 CRYST1 47.413 47.237 51.462 90.00 103.13 90.00 P 1 21 1 2 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 0.021091 0.000000 0.004919 0.00000 SCALE2 0.000000 0.021170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019953 0.00000