HEADER OXIDOREDUCTASE 01-APR-09 3GWL TITLE CRYSTAL STRUCTURE OF ASFV PB119L, A VIRAL SULFHYDRYL OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAD-LINKED SULFHYDRYL OXIDASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-103; COMPND 5 SYNONYM: P14; COMPND 6 EC: 1.8.3.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS BA71V; SOURCE 3 ORGANISM_COMMON: ASFV; SOURCE 4 ORGANISM_TAXID: 10498; SOURCE 5 STRAIN: BADAJOZ 1971 VERO-ADAPTED, BA71V; SOURCE 6 GENE: 9GL, B119L, BA71V-073; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HOMODIMER, FIVE-HELIX BUNDLE, DISULFIDE BOND, FAD, FLAVOPROTEIN, LATE KEYWDS 2 PROTEIN, OXIDOREDUCTASE, VIRULENCE EXPDTA X-RAY DIFFRACTION AUTHOR M.HAKIM,D.FASS REVDAT 2 07-DEC-16 3GWL 1 JRNL VERSN REVDAT 1 07-JUL-09 3GWL 0 JRNL AUTH M.HAKIM,D.FASS JRNL TITL DIMER INTERFACE MIGRATION IN A VIRAL SULFHYDRYL OXIDASE JRNL REF J.MOL.BIOL. V. 391 758 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19576902 JRNL DOI 10.1016/J.JMB.2009.06.070 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 16030 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1103 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 : 1802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 2.130 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 3GWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-09. REMARK 100 THE RCSB ID CODE IS RCSB052397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16153 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32200 REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH 7.8), 7% (V/V) REMARK 280 ISOPROPANOL, 5% (W/V) PEG 12K, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.22500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.84000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.84000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.50000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 B 98 REMARK 465 SER B 99 REMARK 465 LEU B 202 REMARK 465 LYS B 203 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 LYS A 203 CG CD CE NZ 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 PRO A 143 26.25 -78.31 REMARK 500 ALA B 122 52.96 -149.92 REMARK 500 CYS B 144 118.14 -162.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 335 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GWN RELATED DB: PDB REMARK 900 RELATED ID: 1JR8 RELATED DB: PDB REMARK 900 ERV2P, A YEAST HOMOLOG REMARK 900 RELATED ID: 1OQC RELATED DB: PDB REMARK 900 ALR, A MAMMALIAN HOMOLOG REMARK 900 RELATED ID: 2HJ3 RELATED DB: PDB REMARK 900 ATERV1, A PLANT HOMOLOG DBREF 3GWL A 101 203 UNP Q65163 FLSO_ASFB7 1 103 DBREF 3GWL B 101 203 UNP Q65163 FLSO_ASFB7 1 103 SEQADV 3GWL GLY A 98 UNP Q65163 EXPRESSION TAG SEQADV 3GWL SER A 99 UNP Q65163 EXPRESSION TAG SEQADV 3GWL HIS A 100 UNP Q65163 EXPRESSION TAG SEQADV 3GWL GLY B 98 UNP Q65163 EXPRESSION TAG SEQADV 3GWL SER B 99 UNP Q65163 EXPRESSION TAG SEQADV 3GWL HIS B 100 UNP Q65163 EXPRESSION TAG SEQRES 1 A 106 GLY SER HIS MET LEU HIS TRP GLY PRO LYS TYR TRP ARG SEQRES 2 A 106 SER LEU HIS LEU TYR ALA ILE PHE PHE SER ASP ALA PRO SEQRES 3 A 106 SER TRP LYS GLU LYS TYR GLU ALA ILE GLN TRP ILE LEU SEQRES 4 A 106 ASN PHE ILE GLU SER LEU PRO CYS THR ARG CYS GLN HIS SEQRES 5 A 106 HIS ALA PHE SER TYR LEU THR LYS ASN PRO LEU THR LEU SEQRES 6 A 106 ASN ASN SER GLU ASP PHE GLN TYR TRP THR PHE ALA PHE SEQRES 7 A 106 HIS ASN ASN VAL ASN ASN ARG LEU ASN LYS LYS ILE ILE SEQRES 8 A 106 SER TRP SER GLU TYR LYS ASN ILE TYR GLU GLN SER ILE SEQRES 9 A 106 LEU LYS SEQRES 1 B 106 GLY SER HIS MET LEU HIS TRP GLY PRO LYS TYR TRP ARG SEQRES 2 B 106 SER LEU HIS LEU TYR ALA ILE PHE PHE SER ASP ALA PRO SEQRES 3 B 106 SER TRP LYS GLU LYS TYR GLU ALA ILE GLN TRP ILE LEU SEQRES 4 B 106 ASN PHE ILE GLU SER LEU PRO CYS THR ARG CYS GLN HIS SEQRES 5 B 106 HIS ALA PHE SER TYR LEU THR LYS ASN PRO LEU THR LEU SEQRES 6 B 106 ASN ASN SER GLU ASP PHE GLN TYR TRP THR PHE ALA PHE SEQRES 7 B 106 HIS ASN ASN VAL ASN ASN ARG LEU ASN LYS LYS ILE ILE SEQRES 8 B 106 SER TRP SER GLU TYR LYS ASN ILE TYR GLU GLN SER ILE SEQRES 9 B 106 LEU LYS HET FAD A 334 53 HET FAD B 335 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 5 HOH *177(H2 O) HELIX 1 1 HIS A 100 PHE A 119 1 20 HELIX 2 2 SER A 124 LEU A 142 1 19 HELIX 3 3 CYS A 144 ASN A 158 1 15 HELIX 4 4 ASN A 164 LEU A 183 1 20 HELIX 5 5 SER A 189 GLU A 198 1 10 HELIX 6 6 HIS B 100 PHE B 118 1 19 HELIX 7 7 SER B 124 LEU B 142 1 19 HELIX 8 8 CYS B 144 ASN B 158 1 15 HELIX 9 9 ASN B 164 LEU B 183 1 20 HELIX 10 10 SER B 189 TYR B 197 1 9 SSBOND 1 CYS A 144 CYS A 147 1555 1555 2.03 SSBOND 2 CYS B 144 CYS B 147 1555 1555 2.04 SITE 1 AC1 29 HOH A 34 HOH A 53 HOH A 54 HOH A 55 SITE 2 AC1 29 HOH A 58 MET A 101 LEU A 102 GLY A 105 SITE 3 AC1 29 PRO A 106 TYR A 108 TRP A 109 HIS A 113 SITE 4 AC1 29 LEU A 142 ARG A 146 CYS A 147 PHE A 173 SITE 5 AC1 29 PHE A 175 HIS A 176 ASN A 177 VAL A 179 SITE 6 AC1 29 ASN A 180 ARG A 182 LYS A 185 ILE A 188 SITE 7 AC1 29 TYR A 193 ILE A 196 HOH A 222 HOH A 241 SITE 8 AC1 29 HOH B 7 SITE 1 AC2 29 TRP A 190 HOH B 13 HOH B 19 HOH B 21 SITE 2 AC2 29 HOH B 24 HOH B 92 MET B 101 GLY B 105 SITE 3 AC2 29 PRO B 106 TYR B 108 TRP B 109 HIS B 113 SITE 4 AC2 29 LEU B 142 ARG B 146 CYS B 147 HIS B 150 SITE 5 AC2 29 PHE B 173 PHE B 175 HIS B 176 ASN B 177 SITE 6 AC2 29 VAL B 179 ASN B 180 ARG B 182 LEU B 183 SITE 7 AC2 29 LYS B 185 ILE B 188 TYR B 193 HOH B 217 SITE 8 AC2 29 HOH B 224 CRYST1 46.450 69.000 83.680 90.00 90.00 90.00 P 21 21 21 8 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 0.021529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011950 0.00000