HEADER HYDROLASE 16-JUL-12 4B2L TITLE HUMANISED MONOMERIC RADA IN COMPLEX WITH L-METHYLESTER TRYPTOPHAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR AND RECOMBINATION PROTEIN RADA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ATPASE, RESIDUES 108-349; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: CONTAINING PUBS520 PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS HYDROLASE, RECOMBINASE, THERMOSTABLE, PEPTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.E.SCOTT,M.T.EHEBAUER,T.PUKALA,M.MARSH,T.L.BLUNDELL, AUTHOR 2 A.R.VENKITARAMAN,C.ABELL,M.HYVONEN REVDAT 3 20-DEC-23 4B2L 1 REMARK REVDAT 2 27-FEB-13 4B2L 1 JRNL REVDAT 1 06-FEB-13 4B2L 0 JRNL AUTH D.E.SCOTT,M.T.EHEBAUER,T.PUKALA,M.MARSH,T.L.BLUNDELL, JRNL AUTH 2 A.R.VENKITARAMAN,C.ABELL,M.HYVONEN JRNL TITL USING A FRAGMENT-BASED APPROACH TO TARGET PROTEIN-PROTEIN JRNL TITL 2 INTERACTIONS. JRNL REF CHEMBIOCHEM V. 14 332 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 23344974 JRNL DOI 10.1002/CBIC.201200521 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 31773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1636 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 32.0970 - 3.4315 0.98 2585 138 0.1624 0.1883 REMARK 3 2 3.4315 - 2.7241 0.98 2563 134 0.1751 0.1985 REMARK 3 3 2.7241 - 2.3799 0.98 2536 133 0.1785 0.2051 REMARK 3 4 2.3799 - 2.1623 0.98 2574 130 0.1837 0.2312 REMARK 3 5 2.1623 - 2.0074 0.98 2481 152 0.1873 0.2405 REMARK 3 6 2.0074 - 1.8890 0.97 2535 122 0.1955 0.2338 REMARK 3 7 1.8890 - 1.7944 0.97 2491 144 0.2018 0.2499 REMARK 3 8 1.7944 - 1.7163 0.97 2520 129 0.2012 0.2440 REMARK 3 9 1.7163 - 1.6503 0.96 2491 130 0.2175 0.2723 REMARK 3 10 1.6503 - 1.5933 0.97 2497 135 0.2276 0.2645 REMARK 3 11 1.5933 - 1.5435 0.96 2466 151 0.2397 0.2761 REMARK 3 12 1.5435 - 1.4994 0.94 2398 138 0.2564 0.2989 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 : 0.34 REMARK 3 B_SOL : 42.54 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.86740 REMARK 3 B22 (A**2) : -0.23300 REMARK 3 B33 (A**2) : -0.63440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.89250 REMARK 3 B23 (A**2) : 0.00000 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 1769 REMARK 3 ANGLE : 1.545 2387 REMARK 3 CHIRALITY : 0.144 272 REMARK 3 PLANARITY : 0.004 310 REMARK 3 DIHEDRAL : 17.008 662 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 4B2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1290053371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31779 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.78 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PZN CHAIN A REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-15% PEG-1000, 50 MM NAKPHOSPHATE PH REMARK 280 6.2 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 39.38500 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 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 107 REMARK 465 GLN A 286 REMARK 465 ALA A 287 REMARK 465 ASN A 300 REMARK 465 GLY A 301 REMARK 465 GLY A 302 REMARK 465 HIS A 303 REMARK 465 ILE A 304 REMARK 465 LEU A 305 REMARK 465 ALA A 306 REMARK 465 HIS A 307 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2134 DISTANCE = 6.26 ANGSTROMS 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 1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TR7 A 1351 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PZN RELATED DB: PDB REMARK 900 RAD51 (RADA) REMARK 900 RELATED ID: 4A6P RELATED DB: PDB REMARK 900 RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS REMARK 900 RELATED ID: 4A6X RELATED DB: PDB REMARK 900 RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ATP REMARK 900 RELATED ID: 4A74 RELATED DB: PDB REMARK 900 RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO REMARK 900 AMPPNP REMARK 900 RELATED ID: 4A7O RELATED DB: PDB REMARK 900 RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP REMARK 900 RELATED ID: 4B2I RELATED DB: PDB REMARK 900 HUMANISED MONOMERIC RADA IN COMPLEX WITH INDAZOLE DBREF 4B2L A 108 349 UNP O74036 RADA_PYRFU 108 349 SEQADV 4B2L MET A 107 UNP O74036 EXPRESSION TAG SEQADV 4B2L MET A 169 UNP O74036 ILE 169 ENGINEERED MUTATION SEQADV 4B2L ALA A 201 UNP O74036 TYR 201 ENGINEERED MUTATION SEQADV 4B2L TYR A 202 UNP O74036 VAL 202 ENGINEERED MUTATION SEQADV 4B2L MET A 221 UNP O74036 LYS 221 ENGINEERED MUTATION SEQADV 4B2L A UNP O74036 ARG 288 DELETION SEQADV 4B2L A UNP O74036 PRO 289 DELETION SEQADV 4B2L A UNP O74036 ASP 290 DELETION SEQADV 4B2L A UNP O74036 ALA 291 DELETION SEQADV 4B2L A UNP O74036 PHE 292 DELETION SEQADV 4B2L A UNP O74036 PHE 293 DELETION SEQADV 4B2L A UNP O74036 GLY 294 DELETION SEQADV 4B2L A UNP O74036 ASP 295 DELETION SEQADV 4B2L A UNP O74036 PRO 296 DELETION SEQADV 4B2L A UNP O74036 THR 297 DELETION SEQADV 4B2L A UNP O74036 ARG 298 DELETION SEQADV 4B2L A UNP O74036 PRO 299 DELETION SEQADV 4B2L ASN A 300 UNP O74036 ILE 300 ENGINEERED MUTATION SEQRES 1 A 231 MET ALA THR ILE GLY ARG ILE SER THR GLY SER LYS SER SEQRES 2 A 231 LEU ASP LYS LEU LEU GLY GLY GLY ILE GLU THR GLN ALA SEQRES 3 A 231 ILE THR GLU VAL PHE GLY GLU PHE GLY SER GLY LYS THR SEQRES 4 A 231 GLN LEU ALA HIS THR LEU ALA VAL MET VAL GLN LEU PRO SEQRES 5 A 231 PRO GLU GLU GLY GLY LEU ASN GLY SER VAL MET TRP ILE SEQRES 6 A 231 ASP THR GLU ASN THR PHE ARG PRO GLU ARG ILE ARG GLU SEQRES 7 A 231 ILE ALA GLN ASN ARG GLY LEU ASP PRO ASP GLU VAL LEU SEQRES 8 A 231 LYS HIS ILE ALA TYR ALA ARG ALA PHE ASN SER ASN HIS SEQRES 9 A 231 GLN MET LEU LEU VAL GLN GLN ALA GLU ASP MET ILE LYS SEQRES 10 A 231 GLU LEU LEU ASN THR ASP ARG PRO VAL LYS LEU LEU ILE SEQRES 11 A 231 VAL ASP SER LEU THR SER HIS PHE ARG SER GLU TYR ILE SEQRES 12 A 231 GLY ARG GLY ALA LEU ALA GLU ARG GLN GLN LYS LEU ALA SEQRES 13 A 231 LYS HIS LEU ALA ASP LEU HIS ARG LEU ALA ASN LEU TYR SEQRES 14 A 231 ASP ILE ALA VAL PHE VAL THR ASN GLN VAL GLN ALA ASN SEQRES 15 A 231 GLY GLY HIS ILE LEU ALA HIS SER ALA THR LEU ARG VAL SEQRES 16 A 231 TYR LEU ARG LYS GLY LYS GLY GLY LYS ARG ILE ALA ARG SEQRES 17 A 231 LEU ILE ASP ALA PRO HIS LEU PRO GLU GLY GLU ALA VAL SEQRES 18 A 231 PHE SER ILE THR GLU LYS GLY ILE GLU ASP HET PO4 A1350 5 HET TR7 A1351 16 HETNAM PO4 PHOSPHATE ION HETNAM TR7 METHYL L-TRYPTOPHANATE FORMUL 2 PO4 O4 P 3- FORMUL 3 TR7 C12 H14 N2 O2 FORMUL 4 HOH *279(H2 O) HELIX 1 1 SER A 117 LEU A 124 1 8 HELIX 2 2 GLY A 143 VAL A 155 1 13 HELIX 3 3 PRO A 158 GLY A 162 5 5 HELIX 4 4 ARG A 178 ARG A 189 1 12 HELIX 5 5 ASP A 192 HIS A 199 1 8 HELIX 6 6 ASN A 207 LEU A 226 1 20 HELIX 7 7 THR A 241 TYR A 248 1 8 HELIX 8 8 GLY A 250 TYR A 275 1 26 SHEET 1 AA 2 ARG A 112 ILE A 113 0 SHEET 2 AA 2 ILE A 128 GLU A 129 -1 O ILE A 128 N ILE A 113 SHEET 1 AB 9 ILE A 200 ARG A 204 0 SHEET 2 AB 9 SER A 167 ASP A 172 1 O VAL A 168 N ALA A 201 SHEET 3 AB 9 VAL A 232 ASP A 238 1 N LYS A 233 O SER A 167 SHEET 4 AB 9 ALA A 278 ASN A 283 1 O ALA A 278 N LEU A 235 SHEET 5 AB 9 ALA A 132 PHE A 137 1 O ALA A 132 N VAL A 279 SHEET 6 AB 9 LEU A 311 LYS A 317 1 O LEU A 311 N GLU A 135 SHEET 7 AB 9 ARG A 323 ILE A 328 -1 O ILE A 324 N ARG A 316 SHEET 8 AB 9 GLY A 336 THR A 343 -1 O GLY A 336 N LEU A 327 SHEET 9 AB 9 GLY A 346 GLU A 348 -1 O GLY A 346 N THR A 343 CISPEP 1 ASP A 238 SER A 239 0 6.38 CISPEP 2 SER A 308 ALA A 309 0 3.11 SITE 1 AC1 8 GLY A 141 SER A 142 GLY A 143 LYS A 144 SITE 2 AC1 8 THR A 145 GLN A 146 HOH A2048 HOH A2050 SITE 1 AC2 9 MET A 169 ALA A 201 ALA A 203 LEU A 214 SITE 2 AC2 9 GLN A 217 ALA A 218 ASP A 220 MET A 221 SITE 3 AC2 9 HIS A 332 CRYST1 37.620 78.770 39.630 90.00 118.06 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 0.026582 0.000000 0.014169 0.00000 SCALE2 0.000000 0.012695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028595 0.00000