HEADER HYDROLASE 09-FEB-13 4J5Q TITLE TARG1 (C6ORF130), TERMINAL ADP-RIBOSE GLYCOHYDROLASE 1, APO STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-ACETYL-ADP-RIBOSE DEACETYLASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: C6ORF130, OARD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS DNA REPAIR, CELLULAR SIGNALLING, MACRO DOMAIN, GLYCOHYDROLASE, POLY- KEYWDS 2 ADP RIBOSE, PARP, ADP-RIBOSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,C.D.APPEL,J.KRAHN,R.S.WILLIAMS REVDAT 4 20-SEP-23 4J5Q 1 REMARK REVDAT 3 03-JUL-13 4J5Q 1 JRNL REVDAT 2 01-MAY-13 4J5Q 1 JRNL REVDAT 1 27-MAR-13 4J5Q 0 JRNL AUTH R.SHARIFI,R.MORRA,C.D.APPEL,M.TALLIS,B.CHIOZA,G.JANKEVICIUS, JRNL AUTH 2 M.A.SIMPSON,I.MATIC,E.OZKAN,B.GOLIA,M.J.SCHELLENBERG, JRNL AUTH 3 R.WESTON,J.G.WILLIAMS,M.N.ROSSI,H.GALEHDARI,J.KRAHN,A.WAN, JRNL AUTH 4 R.C.TREMBATH,A.H.CROSBY,D.AHEL,R.HAY,A.G.LADURNER, JRNL AUTH 5 G.TIMINSZKY,R.S.WILLIAMS,I.AHEL JRNL TITL DEFICIENCY OF TERMINAL ADP-RIBOSE PROTEIN GLYCOHYDROLASE JRNL TITL 2 TARG1/C6ORF130 IN NEURODEGENERATIVE DISEASE. JRNL REF EMBO J. V. 32 1225 2013 JRNL REFN ISSN 0261-4189 JRNL PMID 23481255 JRNL DOI 10.1038/EMBOJ.2013.51 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 34392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1756 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 30.0628 - 3.1732 0.92 2437 112 0.1564 0.1744 REMARK 3 2 3.1732 - 2.5191 1.00 2593 146 0.1409 0.1912 REMARK 3 3 2.5191 - 2.2008 1.00 2589 136 0.1181 0.1466 REMARK 3 4 2.2008 - 1.9996 0.99 2576 149 0.1025 0.1278 REMARK 3 5 1.9996 - 1.8563 0.99 2522 152 0.1030 0.1327 REMARK 3 6 1.8563 - 1.7469 0.99 2577 115 0.1073 0.1419 REMARK 3 7 1.7469 - 1.6594 0.99 2545 143 0.1064 0.1397 REMARK 3 8 1.6594 - 1.5872 0.98 2497 130 0.1082 0.1452 REMARK 3 9 1.5872 - 1.5261 0.97 2551 123 0.1112 0.1500 REMARK 3 10 1.5261 - 1.4734 0.97 2511 141 0.1336 0.1658 REMARK 3 11 1.4734 - 1.4273 0.97 2482 156 0.1401 0.1856 REMARK 3 12 1.4273 - 1.3865 0.95 2426 132 0.1616 0.1947 REMARK 3 13 1.3865 - 1.3500 0.91 2330 121 0.1777 0.2015 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32950 REMARK 3 B22 (A**2) : -1.58000 REMARK 3 B33 (A**2) : 1.25050 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.44100 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 : 0.015 1269 REMARK 3 ANGLE : 1.713 1724 REMARK 3 CHIRALITY : 0.109 194 REMARK 3 PLANARITY : 0.010 220 REMARK 3 DIHEDRAL : 13.268 520 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 4J5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077629. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34621 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 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 2JYC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM CITRATE, 20% ISOPROPANOL, REMARK 280 20% PEG 4000 , PH 5.6, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 31.65750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.68600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.65750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.68600 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 262 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 434 LIES ON A SPECIAL POSITION. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4J5R RELATED DB: PDB REMARK 900 RELATED ID: 4J5S RELATED DB: PDB DBREF 4J5Q A 7 152 UNP Q9Y530 OARD1_HUMAN 7 152 SEQRES 1 A 146 GLU ASP PRO GLU GLY SER ARG ILE THR TYR VAL LYS GLY SEQRES 2 A 146 ASP LEU PHE ALA CYS PRO LYS THR ASP SER LEU ALA HIS SEQRES 3 A 146 CYS ILE SER GLU ASP CYS ARG MET GLY ALA GLY ILE ALA SEQRES 4 A 146 VAL LEU PHE LYS LYS LYS PHE GLY GLY VAL GLN GLU LEU SEQRES 5 A 146 LEU ASN GLN GLN LYS LYS SER GLY GLU VAL ALA VAL LEU SEQRES 6 A 146 LYS ARG ASP GLY ARG TYR ILE TYR TYR LEU ILE THR LYS SEQRES 7 A 146 LYS ARG ALA SER HIS LYS PRO THR TYR GLU ASN LEU GLN SEQRES 8 A 146 LYS SER LEU GLU ALA MET LYS SER HIS CYS LEU LYS ASN SEQRES 9 A 146 GLY VAL THR ASP LEU SER MET PRO ARG ILE GLY CYS GLY SEQRES 10 A 146 LEU ASP ARG LEU GLN TRP GLU ASN VAL SER ALA MET ILE SEQRES 11 A 146 GLU GLU VAL PHE GLU ALA THR ASP ILE LYS ILE THR VAL SEQRES 12 A 146 TYR THR LEU FORMUL 2 HOH *235(H2 O) HELIX 1 1 ASP A 20 CYS A 24 5 5 HELIX 2 2 ILE A 44 GLY A 53 1 10 HELIX 3 3 GLY A 54 GLN A 61 1 8 HELIX 4 4 THR A 92 GLY A 111 1 20 HELIX 5 5 CYS A 122 ARG A 126 5 5 HELIX 6 6 GLN A 128 GLU A 141 1 14 SHEET 1 A 6 ILE A 14 LYS A 18 0 SHEET 2 A 6 LYS A 146 THR A 151 1 O VAL A 149 N THR A 15 SHEET 3 A 6 ASP A 114 MET A 117 1 N LEU A 115 O LYS A 146 SHEET 4 A 6 SER A 29 SER A 35 1 N SER A 29 O SER A 116 SHEET 5 A 6 ARG A 76 LYS A 84 1 O TYR A 79 N LEU A 30 SHEET 6 A 6 GLU A 67 ARG A 73 -1 N ALA A 69 O TYR A 80 CRYST1 63.315 75.372 35.000 90.00 100.63 90.00 C 1 2 1 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 0.015794 0.000000 0.002964 0.00000 SCALE2 0.000000 0.013268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029070 0.00000