HEADER HYDROLASE 04-AUG-08 3E1U TITLE THE CRYSTAL STRUCTURE OF THE ANTI-VIRAL APOBEC3G CATALYTIC DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3G; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APOBEC3G CATALYTIC DOMAIN (UNP RESIDUES 197-380); 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: APOBEC3G, MDS019; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XA-90; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS FIVE BETA-STRANDS SURROUNDED BY SIX ALPHA-HELICES, ALTERNATIVE KEYWDS 2 SPLICING, ANTIVIRAL DEFENSE, CYTOPLASM, HOST-VIRUS INTERACTION, KEYWDS 3 HYDROLASE, METAL-BINDING, NUCLEUS, POLYMORPHISM, UBL CONJUGATION, KEYWDS 4 ZINC EXPDTA X-RAY DIFFRACTION AUTHOR L.HOLDEN,C.PROCHNOW,Y.P.CHANG,R.BRANSTEITTER,L.CHELICO,U.SEN, AUTHOR 2 R.C.STEVENS,R.F.GOODMAN,X.S.CHEN REVDAT 4 21-FEB-24 3E1U 1 REMARK SEQADV REVDAT 3 24-FEB-09 3E1U 1 VERSN REVDAT 2 11-NOV-08 3E1U 1 JRNL REVDAT 1 07-OCT-08 3E1U 0 JRNL AUTH L.G.HOLDEN,C.PROCHNOW,Y.P.CHANG,R.BRANSTEITTER,L.CHELICO, JRNL AUTH 2 U.SEN,R.C.STEVENS,M.F.GOODMAN,X.S.CHEN JRNL TITL CRYSTAL STRUCTURE OF THE ANTI-VIRAL APOBEC3G CATALYTIC JRNL TITL 2 DOMAIN AND FUNCTIONAL IMPLICATIONS. JRNL REF NATURE V. 456 121 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18849968 JRNL DOI 10.1038/NATURE07357 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.700 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15669 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1511 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1523 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3E1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792060, 0.9790670 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17604 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 9.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MES PH 6.5, 40% PEG 200, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.73200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.66450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.73200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.66450 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 192 REMARK 465 PRO A 193 REMARK 465 LEU A 194 REMARK 465 GLY A 195 REMARK 465 SER A 196 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 TRP A 211 123.62 -30.00 REMARK 500 HIS A 228 110.33 67.78 REMARK 500 PRO A 267 98.59 -38.60 REMARK 500 PHE A 268 1.16 42.11 REMARK 500 LYS A 270 -134.03 -98.51 REMARK 500 ASP A 272 -81.29 84.60 REMARK 500 LEU A 273 -31.57 86.70 REMARK 500 LYS A 303 -35.74 65.96 REMARK 500 ILE A 314 102.54 69.98 REMARK 500 ASP A 316 89.19 48.68 REMARK 500 GLN A 318 -4.67 69.50 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 257 ND1 REMARK 620 2 CYS A 288 SG 115.7 REMARK 620 3 CYS A 291 SG 111.0 115.9 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 1001 DBREF 3E1U A 197 380 UNP Q9HC16 ABC3G_HUMAN 197 380 SEQADV 3E1U GLY A 192 UNP Q9HC16 EXPRESSION TAG SEQADV 3E1U PRO A 193 UNP Q9HC16 EXPRESSION TAG SEQADV 3E1U LEU A 194 UNP Q9HC16 EXPRESSION TAG SEQADV 3E1U GLY A 195 UNP Q9HC16 EXPRESSION TAG SEQADV 3E1U SER A 196 UNP Q9HC16 EXPRESSION TAG SEQRES 1 A 189 GLY PRO LEU GLY SER MET ASP PRO PRO THR PHE THR PHE SEQRES 2 A 189 ASN PHE ASN ASN GLU PRO TRP VAL ARG GLY ARG HIS GLU SEQRES 3 A 189 THR TYR LEU CYS TYR GLU VAL GLU ARG MET HIS ASN ASP SEQRES 4 A 189 THR TRP VAL LEU LEU ASN GLN ARG ARG GLY PHE LEU CYS SEQRES 5 A 189 ASN GLN ALA PRO HIS LYS HIS GLY PHE LEU GLU GLY ARG SEQRES 6 A 189 HIS ALA GLU LEU CYS PHE LEU ASP VAL ILE PRO PHE TRP SEQRES 7 A 189 LYS LEU ASP LEU ASP GLN ASP TYR ARG VAL THR CYS PHE SEQRES 8 A 189 THR SER TRP SER PRO CYS PHE SER CYS ALA GLN GLU MET SEQRES 9 A 189 ALA LYS PHE ILE SER LYS ASN LYS HIS VAL SER LEU CYS SEQRES 10 A 189 ILE PHE THR ALA ARG ILE TYR ASP ASP GLN GLY ARG CYS SEQRES 11 A 189 GLN GLU GLY LEU ARG THR LEU ALA GLU ALA GLY ALA LYS SEQRES 12 A 189 ILE SER ILE MET THR TYR SER GLU PHE LYS HIS CYS TRP SEQRES 13 A 189 ASP THR PHE VAL ASP HIS GLN GLY CYS PRO PHE GLN PRO SEQRES 14 A 189 TRP ASP GLY LEU ASP GLU HIS SER GLN ASP LEU SER GLY SEQRES 15 A 189 ARG LEU ARG ALA ILE LEU GLN HET ZN A1001 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *30(H2 O) HELIX 1 1 ASP A 198 ASN A 207 1 10 HELIX 2 2 HIS A 257 ILE A 266 1 10 HELIX 3 3 CYS A 288 LYS A 303 1 16 HELIX 4 4 ARG A 320 ALA A 331 1 12 HELIX 5 5 THR A 339 VAL A 351 1 13 HELIX 6 6 GLY A 363 GLN A 380 1 18 SHEET 1 A 5 LEU A 235 CYS A 243 0 SHEET 2 A 5 TYR A 219 ARG A 226 -1 N TYR A 222 O GLY A 240 SHEET 3 A 5 TYR A 277 THR A 283 -1 O ARG A 278 N GLU A 225 SHEET 4 A 5 VAL A 305 THR A 311 1 O PHE A 310 N CYS A 281 SHEET 5 A 5 LYS A 334 ILE A 337 1 O LYS A 334 N ILE A 309 LINK ND1 HIS A 257 ZN ZN A1001 1555 1555 2.25 LINK SG CYS A 288 ZN ZN A1001 1555 1555 2.36 LINK SG CYS A 291 ZN ZN A1001 1555 1555 2.30 SITE 1 AC1 4 HOH A 26 HIS A 257 CYS A 288 CYS A 291 CRYST1 83.464 57.329 40.578 90.00 96.46 90.00 C 1 2 1 4 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 0.011981 0.000000 0.001357 0.00000 SCALE2 0.000000 0.017443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024801 0.00000