HEADER HYDROLASE 18-JUN-11 3SIJ TITLE THE X-RAY CRYSTAL STRUCTURE OF POLY(ADP-RIBOSE) GLYCOHYDROLASE E115A TITLE 2 MUTANT FROM THERMOMONOSPORA CURVATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(ADP-RIBOSE) GLYCOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PARG; COMPND 5 EC: 3.2.1.143; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOMONOSPORA CURVATA; SOURCE 3 ORGANISM_TAXID: 471852; SOURCE 4 STRAIN: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081; SOURCE 5 GENE: TCUR_1721; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.DUNSTAN,D.LEYS REVDAT 5 13-SEP-23 3SIJ 1 SEQADV REVDAT 4 12-OCT-11 3SIJ 1 JRNL REVDAT 3 28-SEP-11 3SIJ 1 JRNL REVDAT 2 31-AUG-11 3SIJ 1 JRNL REVDAT 1 24-AUG-11 3SIJ 0 JRNL AUTH D.SLADE,M.S.DUNSTAN,E.BARKAUSKAITE,R.WESTON,P.LAFITE, JRNL AUTH 2 N.DIXON,M.AHEL,D.LEYS,I.AHEL JRNL TITL THE STRUCTURE AND CATALYTIC MECHANISM OF A POLY(ADP-RIBOSE) JRNL TITL 2 GLYCOHYDROLASE. JRNL REF NATURE V. 477 616 2011 JRNL REFN ISSN 0028-0836 JRNL PMID 21892188 JRNL DOI 10.1038/NATURE10404 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 18831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 975 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 45.2636 - 3.6341 0.99 2731 132 0.1640 0.1868 REMARK 3 2 3.6341 - 2.8846 0.99 2601 143 0.1729 0.2183 REMARK 3 3 2.8846 - 2.5200 0.99 2531 152 0.1900 0.2593 REMARK 3 4 2.5200 - 2.2896 0.98 2499 139 0.1815 0.2693 REMARK 3 5 2.2896 - 2.1255 0.99 2546 136 0.1815 0.2363 REMARK 3 6 2.1255 - 2.0002 0.98 2478 129 0.1896 0.2526 REMARK 3 7 2.0002 - 1.9000 0.97 2467 144 0.2221 0.2969 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 44.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29510 REMARK 3 B22 (A**2) : 1.33680 REMARK 3 B33 (A**2) : -1.04170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.007 2073 REMARK 3 ANGLE : 1.015 2813 REMARK 3 CHIRALITY : 0.069 303 REMARK 3 PLANARITY : 0.004 377 REMARK 3 DIHEDRAL : 13.039 744 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.8747 -13.8630 -13.2311 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.1446 REMARK 3 T33: 0.1174 T12: -0.0350 REMARK 3 T13: -0.0041 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.6512 L22: 1.0635 REMARK 3 L33: 1.1406 L12: -0.7923 REMARK 3 L13: 0.4595 L23: -0.1204 REMARK 3 S TENSOR REMARK 3 S11: 0.0539 S12: 0.1312 S13: -0.0053 REMARK 3 S21: -0.0384 S22: -0.1115 S23: 0.0320 REMARK 3 S31: -0.2542 S32: 0.2816 S33: 0.0284 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 3SIJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PHENIX REMARK 200 DATA SCALING SOFTWARE : PHENIX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18831 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 45.251 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3SIG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG6000, 0.1 M BICINE, PH 9.0, REMARK 280 SITTING DROP, VAPOR DIFFUSION 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 25.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.71500 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: 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 LEU A 58 REMARK 465 GLY A 59 REMARK 465 ALA A 60 REMARK 465 ALA A 61 REMARK 465 SER A 62 REMARK 465 ASP A 63 REMARK 465 GLY A 64 REMARK 465 ALA A 65 REMARK 465 PRO A 66 REMARK 465 GLY A 277 REMARK 465 SER A 278 REMARK 465 LEU A 279 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 3 CG CD NE CZ NH1 NH2 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 TYR A 145 -138.99 54.61 REMARK 500 PHE A 158 12.76 -145.92 REMARK 500 LEU A 219 -167.28 -112.75 REMARK 500 ASP A 244 49.99 38.95 REMARK 500 ALA A 263 151.28 -47.74 REMARK 500 ALA A 266 66.44 29.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SIG RELATED DB: PDB REMARK 900 THE X-RAY CRYSTAL STRUCTURE OF POLY(ADP-RIBOSE) GLYCOHYDROLASE REMARK 900 (PARG) BOUND TO ADP-RIBOSE FROM THERMOMONOSPORA CURVATA REMARK 900 RELATED ID: 3SIH RELATED DB: PDB REMARK 900 THE X-RAY CRYSTAL STRUCTURE OF POLY(ADP-RIBOSE) GLYCOHYDROLASE REMARK 900 (PARG) FROM THERMOMONOSPORA CURVATA REMARK 900 RELATED ID: 3SII RELATED DB: PDB REMARK 900 THE X-RAY CRYSTAL STRUCTURE OF POLY(ADP-RIBOSE) GLYCOHYDROLASE REMARK 900 BOUND TO THE INHIBITOR ADP-HPD FROM THERMOMONOSPORA CURVATA DBREF 3SIJ A 3 279 UNP D1AC29 D1AC29_THECD 40 316 SEQADV 3SIJ ALA A 115 UNP D1AC29 GLU 152 ENGINEERED MUTATION SEQRES 1 A 277 ARG HIS SER ARG ARG ALA ILE ALA ALA GLU THR VAL GLU SEQRES 2 A 277 ILE LEU GLU ARG GLY ARG TYR THR ALA PRO SER GLY ARG SEQRES 3 A 277 VAL VAL PRO ILE ALA ASP HIS VAL ALA GLN ALA VAL ARG SEQRES 4 A 277 GLY THR ARG LEU TYR ARG PRO GLU LYS LEU ALA VAL LEU SEQRES 5 A 277 LEU GLU GLY LEU GLY ALA ALA SER ASP GLY ALA PRO THR SEQRES 6 A 277 ARG ILE GLU VAL THR GLU GLU THR THR LEU ALA ALA ALA SEQRES 7 A 277 ARG ARG LEU THR GLY ALA ALA GLY ASP GLN VAL ALA CYS SEQRES 8 A 277 LEU ASN PHE ALA SER ALA GLU HIS PRO GLY GLY GLY PHE SEQRES 9 A 277 LEU SER GLY ALA HIS ALA GLN GLU ALA GLY LEU ALA ARG SEQRES 10 A 277 SER SER GLY LEU TYR ALA SER LEU ARG ALA VAL PRO GLN SEQRES 11 A 277 PHE TYR ALA PHE HIS HIS ARG GLN ARG ASP PRO LEU TYR SEQRES 12 A 277 SER ASP HIS LEU ILE TYR SER PRO GLY VAL PRO VAL PHE SEQRES 13 A 277 ARG ASP ASP ALA GLY ARG LEU LEU GLU GLU PRO TYR ARG SEQRES 14 A 277 VAL ALA PHE LEU THR SER PRO ALA PRO ASN ARG ARG ALA SEQRES 15 A 277 ILE GLY ASP LEU ARG THR VAL GLU GLU ILE GLY ARG VAL SEQRES 16 A 277 LEU ARG GLY ARG ALA ALA LYS VAL LEU ALA ALA ALA ARG SEQRES 17 A 277 HIS HIS GLY HIS ARG ARG LEU VAL LEU GLY ALA TRP GLY SEQRES 18 A 277 CYS GLY VAL PHE GLY ASN ASP PRO ALA GLN VAL ALA GLU SEQRES 19 A 277 THR PHE ALA GLY LEU LEU LEU ASP GLY GLY PRO PHE ALA SEQRES 20 A 277 GLY ARG PHE ALA HIS VAL VAL PHE ALA VAL TRP ASP THR SEQRES 21 A 277 ALA PRO GLY ALA PRO ARG HIS ALA ALA PHE ALA ARG ARG SEQRES 22 A 277 PHE GLY SER LEU FORMUL 2 HOH *123(H2 O) HELIX 1 1 ARG A 3 GLY A 20 1 18 HELIX 2 2 ILE A 32 GLY A 42 1 11 HELIX 3 3 ARG A 47 GLY A 57 1 11 HELIX 4 4 THR A 75 ALA A 87 1 13 HELIX 5 5 GLY A 105 GLY A 109 5 5 HELIX 6 6 ALA A 112 SER A 121 1 10 HELIX 7 7 GLY A 122 ARG A 128 1 7 HELIX 8 8 VAL A 130 ARG A 141 1 12 HELIX 9 9 ASN A 181 GLY A 186 1 6 HELIX 10 10 ASP A 187 ARG A 189 5 3 HELIX 11 11 THR A 190 HIS A 212 1 23 HELIX 12 12 ASP A 230 LEU A 243 1 14 HELIX 13 13 ALA A 266 PHE A 276 1 11 SHEET 1 A 2 ARG A 21 THR A 23 0 SHEET 2 A 2 VAL A 29 PRO A 31 -1 O VAL A 30 N TYR A 22 SHEET 1 B 7 ARG A 44 TYR A 46 0 SHEET 2 B 7 LEU A 149 ARG A 159 -1 O LEU A 149 N TYR A 46 SHEET 3 B 7 LEU A 165 SER A 177 -1 O TYR A 170 N VAL A 157 SHEET 4 B 7 ALA A 92 PHE A 96 1 N ASN A 95 O LEU A 175 SHEET 5 B 7 ARG A 216 LEU A 219 1 O VAL A 218 N ALA A 92 SHEET 6 B 7 HIS A 254 ALA A 258 1 O VAL A 256 N LEU A 219 SHEET 7 B 7 ARG A 68 THR A 72 1 N GLU A 70 O PHE A 257 CRYST1 50.100 105.430 44.220 90.00 90.00 90.00 P 21 21 21 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 0.019960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022614 0.00000