HEADER ANTITUMOR PROTEIN 25-DEC-13 4O7K TITLE CRYSTAL STRUCTURE OF ONCOGENIC SUPPRESSION ACTIVITY PROTEIN - A TITLE 2 PLASMID FERTILITY INHIBITION FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN OSA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ONCOGENIC SUPPRESSION ACTIVITY PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 GENE: OSA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PLASMID FERTILITY INHIBITION, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.MAINDOLA,P.GOYAL,A.ARULANDU REVDAT 3 20-MAR-24 4O7K 1 REMARK SEQADV REVDAT 2 24-DEC-14 4O7K 1 JRNL REVDAT 1 05-NOV-14 4O7K 0 JRNL AUTH P.MAINDOLA,R.RAINA,P.GOYAL,K.ATMAKURI,A.OJHA,S.GUPTA, JRNL AUTH 2 P.J.CHRISTIE,L.M.IYER,L.ARAVIND,A.AROCKIASAMY JRNL TITL MULTIPLE ENZYMATIC ACTIVITIES OF PARB/SRX SUPERFAMILY JRNL TITL 2 MEDIATE SEXUAL CONFLICT AMONG CONJUGATIVE PLASMIDS JRNL REF NAT COMMUN V. 5 5322 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 25358815 JRNL DOI 10.1038/NCOMMS6322 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 24031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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 25.5398 - 3.6339 1.00 2832 149 0.1692 0.1886 REMARK 3 2 3.6339 - 2.8856 1.00 2665 132 0.1958 0.2229 REMARK 3 3 2.8856 - 2.5212 0.99 2608 148 0.1994 0.2493 REMARK 3 4 2.5212 - 2.2908 0.99 2581 138 0.1942 0.2629 REMARK 3 5 2.2908 - 2.1267 0.98 2536 155 0.1938 0.2619 REMARK 3 6 2.1267 - 2.0014 0.98 2535 125 0.2203 0.2919 REMARK 3 7 2.0014 - 1.9012 0.97 2516 129 0.2480 0.2983 REMARK 3 8 1.9012 - 1.8185 0.95 2451 142 0.2951 0.3370 REMARK 3 9 1.8185 - 1.7485 0.81 2090 99 0.3324 0.3808 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.19 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 1611 REMARK 3 ANGLE : 0.991 2210 REMARK 3 CHIRALITY : 0.037 241 REMARK 3 PLANARITY : 0.005 285 REMARK 3 DIHEDRAL : 14.768 585 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 4O7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084141. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24068 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.748 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : 0.05700 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELX CDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% ISOPROPANOL, 0.5M LITHIUM REMARK 280 SULPHATE, 0.1M PHOSPHATE-CITRATE BUFFER PH 4.2, 0.2M NDSB-201, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 63.44900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.43450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.43450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.17350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.43450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.43450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.72450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.43450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.43450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.17350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.43450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.43450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.72450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.44900 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: MONOMERIC 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 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 ARG A 185 CD NE CZ NH1 NH2 REMARK 470 LYS A 186 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 HIS A 0 -168.71 -121.69 REMARK 500 ASN A 39 68.22 -113.45 REMARK 500 SER A 114 76.23 -150.95 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 PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OVB RELATED DB: PDB DBREF 4O7K A 1 187 UNP P29772 OSA_SHIFL 3 189 SEQADV 4O7K HIS A -1 UNP P29772 EXPRESSION TAG SEQADV 4O7K HIS A 0 UNP P29772 EXPRESSION TAG SEQADV 4O7K TRP A 4 UNP P29772 ARG 6 ENGINEERED MUTATION SEQADV 4O7K LEU A 188 UNP P29772 EXPRESSION TAG SEQRES 1 A 190 HIS HIS MET LEU LEU TRP ARG ARG CYS ARG ALA TRP LEU SEQRES 2 A 190 GLU ILE ARG ARG LEU ASP LYS GLU LEU ALA GLN SER SER SEQRES 3 A 190 GLY LEU PRO LEU GLU LEU PRO GLN ILE VAL PRO ASN ALA SEQRES 4 A 190 TRP ASN GLU VAL VAL TRP ARG LEU PRO VAL PRO ASN HIS SEQRES 5 A 190 PRO ASP ALA PHE MET THR ALA SER ASN ALA ALA GLN SER SEQRES 6 A 190 ASP PHE ILE VAL TYR VAL ASN GLY LEU ALA PHE TYR ARG SEQRES 7 A 190 ALA TRP LEU ALA LEU GLY VAL GLU ASP SER GLN ALA CYS SEQRES 8 A 190 PRO LEU LYS GLN ASP MET PRO LYS ASP ARG LYS TYR PRO SEQRES 9 A 190 SER SER ALA ALA HIS PHE ALA VAL GLY ILE ASP SER PRO SEQRES 10 A 190 VAL PRO LEU ALA ASP VAL SER PRO THR MET ILE LEU GLY SEQRES 11 A 190 HIS PHE ALA VAL CYS PHE THR ASP GLY MET THR ARG SER SEQRES 12 A 190 MET TRP LEU LEU ALA HIS GLU VAL ALA VAL PHE PRO VAL SEQRES 13 A 190 LEU SER ARG ASP GLU ALA SER ALA VAL MET LEU ALA GLU SEQRES 14 A 190 HIS VAL GLY VAL ALA ALA PRO ILE GLN VAL SER LYS LEU SEQRES 15 A 190 ARG GLU GLN CYS ARG LYS ILE LEU HET PO4 A 201 5 HET PO4 A 202 5 HET CL A 203 1 HET IPA A 204 4 HET IPA A 205 4 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 CL CL 1- FORMUL 5 IPA 2(C3 H8 O) FORMUL 7 HOH *111(H2 O) HELIX 1 1 MET A 1 SER A 23 1 23 HELIX 2 2 GLY A 71 ALA A 80 1 10 HELIX 3 3 LEU A 91 ASP A 98 5 8 HELIX 4 4 LYS A 100 GLY A 111 1 12 HELIX 5 5 GLY A 137 HIS A 147 1 11 HELIX 6 6 ASP A 158 GLY A 170 1 13 HELIX 7 7 VAL A 177 LEU A 188 1 12 SHEET 1 A 4 GLN A 32 ILE A 33 0 SHEET 2 A 4 VAL A 42 LEU A 45 -1 O ARG A 44 N GLN A 32 SHEET 3 A 4 ALA A 53 THR A 56 -1 O ALA A 53 N LEU A 45 SHEET 4 A 4 VAL A 116 PRO A 117 1 O VAL A 116 N PHE A 54 SHEET 1 B 3 VAL A 151 SER A 156 0 SHEET 2 B 3 PHE A 65 ASN A 70 -1 N VAL A 69 O PHE A 152 SHEET 3 B 3 ILE A 175 GLN A 176 -1 O ILE A 175 N ILE A 66 SHEET 1 C 2 ASP A 120 ILE A 126 0 SHEET 2 C 2 HIS A 129 ASP A 136 -1 O THR A 135 N ASP A 120 SITE 1 AC1 6 LYS A 100 GLY A 137 MET A 138 THR A 139 SITE 2 AC1 6 ARG A 140 HOH A 357 SITE 1 AC2 5 HIS A 50 ALA A 105 TRP A 143 HIS A 147 SITE 2 AC2 5 HOH A 332 SITE 1 AC3 5 GLU A 40 VAL A 41 ALA A 57 SER A 58 SITE 2 AC3 5 ARG A 181 SITE 1 AC4 4 HIS A 107 PRO A 117 ARG A 140 HOH A 341 SITE 1 AC5 4 TRP A 4 ARG A 76 HIS A 168 HOH A 330 CRYST1 60.869 60.869 126.898 90.00 90.00 90.00 P 43 21 2 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 0.016429 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016429 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007880 0.00000