HEADER TRANSFERASE 14-MAR-13 4JMP TITLE CRYSTAL STRUCTURE OF THE CHIMERICAL PROTEIN CAPA2B2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TERMINAL FRAGMENT OF CAPA, PROTEIN TYROSINE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MEMBRANE PROTEIN CAPB2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CHIMERA OF CAPA AND PROTEIN TYROSINE KINASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: CAPA2, CAPB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS ROSSMANN FOLD, TYROSINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.OLIVARES-ILLANA,S.MORERA,C.GRANGEASSE,S.NESSLER REVDAT 3 08-NOV-23 4JMP 1 SEQADV REVDAT 2 16-AUG-17 4JMP 1 SOURCE REMARK REVDAT 1 05-FEB-14 4JMP 0 JRNL AUTH J.GRUSZCZYK,V.OLIVARES-ILLANA,J.NOURIKYAN,A.FLEURIE, JRNL AUTH 2 E.BECHET,V.GUEGUEN-CHAIGNON,C.FRETON,M.AUMONT-NICAISE, JRNL AUTH 3 S.MORERA,C.GRANGEASSE,S.NESSLER JRNL TITL COMPARATIVE ANALYSIS OF THE TYR-KINASES CAPB1 AND CAPB2 JRNL TITL 2 FUSED TO THEIR COGNATE MODULATORS CAPA1 AND CAPA2 FROM JRNL TITL 3 STAPHYLOCOCCUS AUREUS JRNL REF PLOS ONE V. 8 75958 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24146800 JRNL DOI 10.1371/JOURNAL.PONE.0075958 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 54245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2748 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 33.0566 - 3.5274 0.89 2393 111 0.1645 0.1564 REMARK 3 2 3.5274 - 2.8003 0.95 2503 142 0.1660 0.1946 REMARK 3 3 2.8003 - 2.4464 0.96 2545 143 0.1759 0.1952 REMARK 3 4 2.4464 - 2.2228 0.97 2569 129 0.1584 0.1781 REMARK 3 5 2.2228 - 2.0635 0.98 2558 137 0.1503 0.1684 REMARK 3 6 2.0635 - 1.9419 0.98 2550 152 0.1589 0.1945 REMARK 3 7 1.9419 - 1.8446 0.98 2571 146 0.1542 0.1783 REMARK 3 8 1.8446 - 1.7643 0.99 2581 138 0.1618 0.1819 REMARK 3 9 1.7643 - 1.6964 0.99 2598 142 0.1591 0.1946 REMARK 3 10 1.6964 - 1.6379 0.99 2597 131 0.1662 0.2096 REMARK 3 11 1.6379 - 1.5867 0.99 2599 135 0.1662 0.1791 REMARK 3 12 1.5867 - 1.5413 0.99 2603 134 0.1741 0.2150 REMARK 3 13 1.5413 - 1.5007 0.99 2590 139 0.1742 0.1911 REMARK 3 14 1.5007 - 1.4641 1.00 2625 139 0.1933 0.2031 REMARK 3 15 1.4641 - 1.4308 1.00 2614 147 0.2001 0.2227 REMARK 3 16 1.4308 - 1.4004 1.00 2568 130 0.2101 0.2218 REMARK 3 17 1.4004 - 1.3724 1.00 2668 146 0.2199 0.2394 REMARK 3 18 1.3724 - 1.3465 1.00 2556 124 0.2295 0.2572 REMARK 3 19 1.3465 - 1.3224 1.00 2648 149 0.2453 0.2674 REMARK 3 20 1.3224 - 1.3000 0.99 2561 134 0.2505 0.2482 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.43 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 1808 REMARK 3 ANGLE : 1.012 2472 REMARK 3 CHIRALITY : 0.069 297 REMARK 3 PLANARITY : 0.005 319 REMARK 3 DIHEDRAL : 11.055 683 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 4JMP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078239. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : HORIZONTALLY DIFFRACTING SI(111) REMARK 200 MONOCHROMATOR AND PT COATED REMARK 200 MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 35.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 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) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.55100 REMARK 200 R SYM FOR SHELL (I) : 0.55100 REMARK 200 FOR SHELL : 2.100 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: 3BFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG550 MME, 100MM HEPES, 5MM REMARK 280 MGCL2, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 290K 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 44.33300 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: 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 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 MET A 182 REMARK 465 ARG A 183 REMARK 465 GLY A 184 REMARK 465 SER A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 GLY A 192 REMARK 465 SER A 193 REMARK 465 LEU A 194 REMARK 465 LEU A 195 REMARK 465 ASP A 196 REMARK 465 LYS A 197 REMARK 465 ARG A 198 REMARK 465 ILE A 199 REMARK 465 LYS A 200 REMARK 465 MET A 1001 REMARK 465 THR A 1002 REMARK 465 ASN A 1003 REMARK 465 THR A 1004 REMARK 465 ARG A 1005 REMARK 465 ARG A 1006 REMARK 465 SER A 1007 REMARK 465 THR A 1008 REMARK 465 ASN A 1036 REMARK 465 ASP A 1216 REMARK 465 LYS A 1217 REMARK 465 SER A 1218 REMARK 465 ALA A 1219 REMARK 465 SER A 1220 REMARK 465 TYR A 1221 REMARK 465 TYR A 1222 REMARK 465 ALA A 1223 REMARK 465 TYR A 1224 REMARK 465 TYR A 1225 REMARK 465 GLY A 1226 REMARK 465 THR A 1227 REMARK 465 ASP A 1228 REMARK 465 GLU A 1229 REMARK 465 SER A 1230 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BFV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CHIMERICAL PROTEIN CAPA1B2 IN COMPLEX WITH REMARK 900 ADP-MG REMARK 900 RELATED ID: 2VED RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE K55M MUTANT OF THE CHIMERICAL PROTEIN REMARK 900 CAPA1B2 REMARK 900 RELATED ID: 4JLV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CHIMERICAL PROTEIN CAPA1B1 IN COMPLEX WITH REMARK 900 ADP-MG DBREF 4JMP A 194 220 UNP Q7BSA3 Q7BSA3_STAAU 194 220 DBREF 4JMP A 1001 1230 UNP A8YPQ5 A8YPQ5_STAAU 1 230 SEQADV 4JMP MET A 182 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP ARG A 183 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP GLY A 184 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP SER A 185 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP HIS A 186 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP HIS A 187 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP HIS A 188 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP HIS A 189 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP HIS A 190 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP HIS A 191 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP GLY A 192 UNP Q7BSA3 EXPRESSION TAG SEQADV 4JMP SER A 193 UNP Q7BSA3 EXPRESSION TAG SEQRES 1 A 269 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER LEU SEQRES 2 A 269 LEU ASP LYS ARG ILE LYS THR GLU GLU ASP VAL GLU SER SEQRES 3 A 269 GLN LEU GLY LEU PRO ILE LEU GLY SER ILE GLN LYS PHE SEQRES 4 A 269 MET THR ASN THR ARG ARG SER THR SER SER LEU ILE VAL SEQRES 5 A 269 HIS GLU GLN PRO LYS SER PRO ILE SER GLU LYS PHE ARG SEQRES 6 A 269 GLY ILE ARG SER ASN ILE MET PHE ALA ASN PRO ASP SER SEQRES 7 A 269 ALA VAL GLN SER ILE VAL ILE THR SER GLU ALA PRO GLY SEQRES 8 A 269 ALA GLY LYS SER THR ILE ALA ALA ASN LEU ALA VAL ALA SEQRES 9 A 269 TYR ALA GLN ALA GLY TYR LYS THR LEU ILE VAL ASP GLY SEQRES 10 A 269 ASP MET ARG LYS PRO THR GLN HIS TYR ILE PHE ASN LEU SEQRES 11 A 269 PRO ASN ASN GLU GLY LEU SER SER LEU LEU LEU ASN TRP SEQRES 12 A 269 SER THR TYR GLN ASP SER ILE ILE SER THR GLU ILE GLU SEQRES 13 A 269 ASP LEU ASP VAL LEU THR SER GLY PRO ILE PRO PRO ASN SEQRES 14 A 269 PRO SER GLU LEU ILE THR SER ARG ALA PHE ALA ASN LEU SEQRES 15 A 269 TYR ASP THR LEU LEU MET ASN TYR ASN PHE VAL ILE ILE SEQRES 16 A 269 ASP THR PRO PRO VAL ASN THR VAL THR ASP ALA GLN LEU SEQRES 17 A 269 PHE SER LYS PHE THR GLY ASN VAL VAL TYR VAL VAL ASN SEQRES 18 A 269 SER GLU ASN ASN ASN LYS ASP GLU VAL LYS LYS GLY LYS SEQRES 19 A 269 GLU LEU ILE GLU ALA THR GLY ALA LYS LEU LEU GLY VAL SEQRES 20 A 269 VAL LEU ASN ARG MET PRO LYS ASP LYS SER ALA SER TYR SEQRES 21 A 269 TYR ALA TYR TYR GLY THR ASP GLU SER FORMUL 2 HOH *207(H2 O) HELIX 1 1 THR A 201 GLY A 210 1 10 HELIX 2 2 LEU A 1011 GLN A 1016 1 6 HELIX 3 3 SER A 1019 ALA A 1035 1 17 HELIX 4 4 GLY A 1054 ALA A 1069 1 16 HELIX 5 5 THR A 1084 PHE A 1089 1 6 HELIX 6 6 GLY A 1096 LEU A 1102 1 7 HELIX 7 7 THR A 1106 SER A 1110 1 5 HELIX 8 8 ASN A 1130 THR A 1136 1 7 HELIX 9 9 SER A 1137 TYR A 1151 1 15 HELIX 10 10 THR A 1165 GLY A 1175 1 11 HELIX 11 11 ASN A 1187 ALA A 1200 1 14 SHEET 1 A 8 ILE A 213 GLN A 218 0 SHEET 2 A 8 LYS A1204 MET A1213 1 O LEU A1210 N ILE A 217 SHEET 3 A 8 ASN A1176 ASN A1182 1 N VAL A1177 O LYS A1204 SHEET 4 A 8 SER A1043 SER A1048 1 N VAL A1045 O VAL A1178 SHEET 5 A 8 PHE A1153 ASP A1157 1 O ILE A1156 N ILE A1044 SHEET 6 A 8 THR A1073 ASP A1077 1 N VAL A1076 O ILE A1155 SHEET 7 A 8 LEU A1119 LEU A1122 1 O LEU A1122 N ASP A1077 SHEET 8 A 8 ILE A1111 SER A1113 -1 N ILE A1112 O VAL A1121 CRYST1 36.332 88.666 39.405 90.00 115.35 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 0.027524 0.000000 0.013040 0.00000 SCALE2 0.000000 0.011278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028081 0.00000