HEADER HYDROLASE 17-JAN-13 3ZJF TITLE A20 OTU DOMAIN WITH IRREVERSIBLY OXIDISED CYS103 FROM 270 MIN H2O2 TITLE 2 SOAK. COMPND MOL_ID: 1; COMPND 2 MOLECULE: A20P50; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: OTU DOMAIN, RESIDUES 1-366; COMPND 5 SYNONYM: TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3, TNF COMPND 6 ALPHA-INDUCED PROTEIN 3, OTU DOMAIN-CONTAINING PROTEIN 7C, COMPND 7 PUTATIVE DNA-BINDING PROTEIN A20, ZINC FINGER PROTEIN A20, A20; COMPND 8 EC: 3.4.19.12, 6.3.2.-; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 OTHER_DETAILS: THE CATALYTIC CYS103 IS IRREVERSIBLY OXIDISED AND COMPND 12 MODELLED AS CYS SULPHINIC ACID (SO2H).; COMPND 13 MOL_ID: 2; COMPND 14 MOLECULE: A20P50; COMPND 15 CHAIN: B; COMPND 16 FRAGMENT: OTU DOMAIN, RESIDUES 1-366; COMPND 17 SYNONYM: TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3, TNF COMPND 18 ALPHA-INDUCED PROTEIN 3, OTU DOMAIN-CONTAINING PROTEIN 7C, COMPND 19 PUTATIVE DNA-BINDING PROTEIN A20, ZINC FINGER PROTEIN A20, A20; COMPND 20 EC: 3.4.19.12, 6.3.2.-; COMPND 21 ENGINEERED: YES; COMPND 22 MUTATION: YES; COMPND 23 OTHER_DETAILS: THE CATALYTIC CYS103 IS IRREVERSIBLY OXIDISED AND COMPND 24 MODELLED AS CYS SULPHONIC ACID (SO3H). SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX6P1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PGEX6P1 KEYWDS HYDROLASE, UBIQUITIN, DEUBIQUITINATING ENZYME, REVERSIBLE OXIDATION, KEYWDS 2 SULPHENIC ACID, CYS PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.KULATHU,F.J.GARCIA,T.E.T.MEVISSEN,M.BUSCH,N.ARNAUDO,K.S.CARROLL, AUTHOR 2 D.BARFORD,D.KOMANDER REVDAT 3 05-NOV-14 3ZJF 1 SEQRES MODRES HET HETNAM REVDAT 3 2 HETSYN FORMUL LINK HETATM REVDAT 3 3 ANISOU REVDAT 2 20-MAR-13 3ZJF 1 JRNL REVDAT 1 06-MAR-13 3ZJF 0 JRNL AUTH Y.KULATHU,F.J.GARCIA,T.E.T.MEVISSEN,M.BUSCH,N.ARNAUDO, JRNL AUTH 2 K.S.CARROLL,D.BARFORD,D.KOMANDER JRNL TITL REGULATION OF A20 AND OTHER OTU DEUBIQUITINASES BY JRNL TITL 2 REVERSIBLE OXIDATION JRNL REF NAT.COMMUN. V. 4 1569 2013 JRNL REFN ISSN 2041-1723 JRNL PMID 23463012 JRNL DOI 10.1038/NCOMMS2567 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.200 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.272 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.00 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.20 REMARK 3 NUMBER OF REFLECTIONS : 45936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1836 REMARK 3 R VALUE (WORKING SET) : 0.1816 REMARK 3 FREE R VALUE : 0.2224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 2327 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 34.2760 - 5.6489 0.93 2512 131 0.1782 0.1899 REMARK 3 2 5.6489 - 4.4869 0.95 2552 146 0.1551 0.2022 REMARK 3 3 4.4869 - 3.9206 0.95 2568 131 0.1449 0.1771 REMARK 3 4 3.9206 - 3.5626 0.96 2591 144 0.1616 0.2071 REMARK 3 5 3.5626 - 3.3074 0.95 2575 127 0.1747 0.2373 REMARK 3 6 3.3074 - 3.1126 0.96 2583 133 0.1900 0.2219 REMARK 3 7 3.1126 - 2.9568 0.95 2545 151 0.1925 0.2219 REMARK 3 8 2.9568 - 2.8281 0.96 2592 142 0.1978 0.2481 REMARK 3 9 2.8281 - 2.7193 0.95 2570 136 0.2030 0.2478 REMARK 3 10 2.7193 - 2.6255 0.95 2604 129 0.1953 0.2363 REMARK 3 11 2.6255 - 2.5434 0.95 2515 144 0.2080 0.2720 REMARK 3 12 2.5434 - 2.4708 0.95 2615 145 0.2129 0.2794 REMARK 3 13 2.4708 - 2.4057 0.95 2539 139 0.2137 0.2879 REMARK 3 14 2.4057 - 2.3471 0.95 2575 135 0.2255 0.2372 REMARK 3 15 2.3471 - 2.2937 0.95 2560 116 0.2305 0.2684 REMARK 3 16 2.2937 - 2.2449 0.95 2599 146 0.2389 0.2670 REMARK 3 17 2.2449 - 2.2000 0.95 2514 132 0.2533 0.3115 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) : 0.27 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.08 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.013 5339 REMARK 3 ANGLE : 1.393 7245 REMARK 3 CHIRALITY : 0.100 813 REMARK 3 PLANARITY : 0.006 917 REMARK 3 DIHEDRAL : 15.648 1965 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -18.4218 28.4253 -13.0677 REMARK 3 T TENSOR REMARK 3 T11: 0.0880 T22: 0.1803 REMARK 3 T33: 0.1506 T12: -0.0660 REMARK 3 T13: -0.0041 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 3.1240 L22: 2.9811 REMARK 3 L33: 4.4325 L12: 0.1985 REMARK 3 L13: 0.2262 L23: -0.7057 REMARK 3 S TENSOR REMARK 3 S11: 0.0521 S12: -0.0686 S13: -0.1404 REMARK 3 S21: 0.3272 S22: -0.0222 S23: -0.1091 REMARK 3 S31: 0.1784 S32: -0.2908 S33: -0.0221 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -12.4878 41.2960 36.0549 REMARK 3 T TENSOR REMARK 3 T11: 0.3530 T22: 0.2020 REMARK 3 T33: 0.2131 T12: 0.1000 REMARK 3 T13: 0.0522 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 2.4963 L22: 2.2697 REMARK 3 L33: 3.2243 L12: 0.2450 REMARK 3 L13: 0.5629 L23: 0.1577 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: 0.1468 S13: 0.2745 REMARK 3 S21: -0.5753 S22: 0.0038 S23: -0.0671 REMARK 3 S31: -0.5620 S32: -0.1885 S33: -0.0130 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIDE CHAINS OF SEVERAL RESIDUES REMARK 3 WERE NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE REMARK 3 MISSING FROM THE STRUCTURE. CYS103 WAS MODELLED AS REMARK 3 SULPHINIC AND SULPHONIC ACID IN CHAIN A AND B, REMARK 3 RESPECTIVELY. SEVERAL RESIDUES WERE MODELLED WITH REMARK 3 WITH OCCUPANCY SET TO 0 OR WITH SIDE CHAINS REMOVED. REMARK 4 REMARK 4 3ZJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JAN-13. REMARK 100 THE PDBE ID CODE IS EBI-55472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45957 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 38.18 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.20 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.0 REMARK 200 R MERGE FOR SHELL (I) : 0.50 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.20 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 2VFJ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-2.5 M NACL, 0.1 M MES [PH REMARK 280 6-6.7]. CRYSTALS WERE SOAKED IN 50 UM H2O2 FOR 270 MIN REMARK 280 PRIOR TO FREEZING AND DATA COLLECTION. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 VAL A 5 REMARK 465 GLN A 150 REMARK 465 GLU A 151 REMARK 465 PHE A 152 REMARK 465 VAL A 153 REMARK 465 GLU A 154 REMARK 465 THR A 155 REMARK 465 GLY A 156 REMARK 465 LEU A 157 REMARK 465 CYS A 158 REMARK 465 TYR A 159 REMARK 465 ASP A 160 REMARK 465 THR A 161 REMARK 465 ARG A 162 REMARK 465 MET A 181 REMARK 465 ALA A 182 REMARK 465 ARG A 183 REMARK 465 SER A 184 REMARK 465 GLY A 185 REMARK 465 MET A 214 REMARK 465 GLU A 219 REMARK 465 SER A 220 REMARK 465 GLY A 221 REMARK 465 SER A 222 REMARK 465 ASN A 223 REMARK 465 PHE A 224 REMARK 465 ALA A 225 REMARK 465 PRO A 226 REMARK 465 LEU A 227 REMARK 465 GLN A 357 REMARK 465 GLU A 358 REMARK 465 ASN A 359 REMARK 465 SER A 360 REMARK 465 GLU A 361 REMARK 465 GLN A 362 REMARK 465 GLY A 363 REMARK 465 ARG A 364 REMARK 465 ARG A 365 REMARK 465 GLU A 366 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 GLN B 4 REMARK 465 VAL B 5 REMARK 465 GLN B 150 REMARK 465 GLU B 151 REMARK 465 PHE B 152 REMARK 465 VAL B 153 REMARK 465 GLU B 154 REMARK 465 THR B 155 REMARK 465 GLY B 156 REMARK 465 LEU B 157 REMARK 465 CYS B 158 REMARK 465 TYR B 159 REMARK 465 ASP B 160 REMARK 465 THR B 161 REMARK 465 ARG B 162 REMARK 465 MET B 181 REMARK 465 ALA B 182 REMARK 465 ARG B 183 REMARK 465 SER B 184 REMARK 465 LEU B 215 REMARK 465 ARG B 216 REMARK 465 SER B 217 REMARK 465 LEU B 218 REMARK 465 GLU B 219 REMARK 465 SER B 220 REMARK 465 GLY B 221 REMARK 465 SER B 222 REMARK 465 ASN B 223 REMARK 465 PHE B 224 REMARK 465 ALA B 225 REMARK 465 PRO B 226 REMARK 465 GLN B 357 REMARK 465 GLU B 358 REMARK 465 ASN B 359 REMARK 465 SER B 360 REMARK 465 GLU B 361 REMARK 465 GLN B 362 REMARK 465 GLY B 363 REMARK 465 ARG B 364 REMARK 465 ARG B 365 REMARK 465 GLU B 366 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 LEU A 6 CG CD1 CD2 REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 ARG A 22 CZ NH1 NH2 REMARK 470 PHE A 56 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 59 CG CD OE1 NE2 REMARK 470 ARG A 87 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 ASP A 134 CG OD1 OD2 REMARK 470 LEU A 147 CG CD1 CD2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 SER A 149 OG REMARK 470 GLU A 167 CD OE1 OE2 REMARK 470 GLU A 192 CD OE1 OE2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 264 CE NZ REMARK 470 SER A 266 OG REMARK 470 ARG A 282 NE CZ NH1 NH2 REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 GLU A 332 CG CD OE1 OE2 REMARK 470 LYS A 337 CG CD CE NZ REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 LYS A 354 CG CD CE NZ REMARK 470 LYS A 355 CG CD CE NZ REMARK 470 TRP A 356 CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 REMARK 470 TRP A 356 CH2 REMARK 470 LEU B 6 CG CD1 CD2 REMARK 470 GLN B 8 CG CD OE1 NE2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 GLN B 55 CG CD OE1 NE2 REMARK 470 PHE B 56 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 59 CG CD OE1 NE2 REMARK 470 PHE B 60 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 ILE B 63 CG1 CG2 CD1 REMARK 470 GLN B 80 CD OE1 NE2 REMARK 470 GLU B 132 CG CD OE1 OE2 REMARK 470 ASP B 134 CG OD1 OD2 REMARK 470 ARG B 136 CD NE CZ NH1 NH2 REMARK 470 ASN B 163 CG OD1 ND2 REMARK 470 ASN B 165 CG OD1 ND2 REMARK 470 ASP B 166 CG OD1 OD2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 THR B 179 OG1 CG2 REMARK 470 GLN B 187 CD OE1 NE2 REMARK 470 LYS B 213 CB CG CD CE NZ REMARK 470 LEU B 227 CG CD1 CD2 REMARK 470 LYS B 228 CG CD CE NZ REMARK 470 GLU B 242 CD OE1 OE2 REMARK 470 LYS B 264 CG CD CE NZ REMARK 470 ASP B 265 CG OD1 OD2 REMARK 470 ARG B 280 CZ NH1 NH2 REMARK 470 ARG B 282 NE CZ NH1 NH2 REMARK 470 LYS B 287 CG CD CE NZ REMARK 470 GLU B 297 CG CD OE1 OE2 REMARK 470 GLU B 300 CG CD OE1 OE2 REMARK 470 LYS B 301 CG CD CE NZ REMARK 470 GLU B 332 CG CD OE1 OE2 REMARK 470 LYS B 337 CG CD CE NZ REMARK 470 GLU B 338 CG CD OE1 OE2 REMARK 470 LYS B 355 CG CD CE NZ REMARK 470 TRP B 356 CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS B 66 NZ LYS B 96 2.02 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 14 78.62 -165.14 REMARK 500 THR A 42 -36.26 -141.29 REMARK 500 PHE A 56 -163.72 -113.88 REMARK 500 ASP A 117 45.75 -84.20 REMARK 500 SER A 266 104.47 -167.59 REMARK 500 ARG A 280 -122.99 53.33 REMARK 500 ARG A 282 -166.41 -119.24 REMARK 500 ASP A 318 -158.65 -114.70 REMARK 500 THR A 321 -23.97 88.49 REMARK 500 LYS A 355 49.34 -82.58 REMARK 500 ASN B 14 84.78 -160.61 REMARK 500 THR B 42 -36.55 -142.54 REMARK 500 GLN B 55 -3.51 70.94 REMARK 500 ASP B 117 41.10 -91.58 REMARK 500 LYS B 213 -68.60 -120.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR B 25 24.8 L L OUTSIDE RANGE 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 CL B1357 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1358 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZJD RELATED DB: PDB REMARK 900 A20 OTU DOMAIN IN REDUCED, ACTIVE STATE AT 1.87 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 3ZJE RELATED DB: PDB REMARK 900 A20 OTU DOMAIN IN REVERSIBLY OXIDISED (SOH) STATE REMARK 900 RELATED ID: 3ZJG RELATED DB: PDB REMARK 900 A20 OTU DOMAIN WITH IRREVERSIBLY OXIDISED CYS103 FROM REMARK 900 60 MIN H2O2 SOAK. DBREF 3ZJF A 1 366 UNP P21580 TNAP3_HUMAN 1 366 DBREF 3ZJF B 1 366 UNP P21580 TNAP3_HUMAN 1 366 SEQADV 3ZJF SER A 114 UNP P21580 GLY 114 ENGINEERED MUTATION SEQADV 3ZJF SER B 114 UNP P21580 GLY 114 ENGINEERED MUTATION SEQRES 1 A 366 MET ALA GLU GLN VAL LEU PRO GLN ALA LEU TYR LEU SER SEQRES 2 A 366 ASN MET ARG LYS ALA VAL LYS ILE ARG GLU ARG THR PRO SEQRES 3 A 366 GLU ASP ILE PHE LYS PRO THR ASN GLY ILE ILE HIS HIS SEQRES 4 A 366 PHE LYS THR MET HIS ARG TYR THR LEU GLU MET PHE ARG SEQRES 5 A 366 THR CYS GLN PHE CYS PRO GLN PHE ARG GLU ILE ILE HIS SEQRES 6 A 366 LYS ALA LEU ILE ASP ARG ASN ILE GLN ALA THR LEU GLU SEQRES 7 A 366 SER GLN LYS LYS LEU ASN TRP CYS ARG GLU VAL ARG LYS SEQRES 8 A 366 LEU VAL ALA LEU LYS THR ASN GLY ASP GLY ASN CSD LEU SEQRES 9 A 366 MET HIS ALA THR SER GLN TYR MET TRP SER VAL GLN ASP SEQRES 10 A 366 THR ASP LEU VAL LEU ARG LYS ALA LEU PHE SER THR LEU SEQRES 11 A 366 LYS GLU THR ASP THR ARG ASN PHE LYS PHE ARG TRP GLN SEQRES 12 A 366 LEU GLU SER LEU LYS SER GLN GLU PHE VAL GLU THR GLY SEQRES 13 A 366 LEU CYS TYR ASP THR ARG ASN TRP ASN ASP GLU TRP ASP SEQRES 14 A 366 ASN LEU ILE LYS MET ALA SER THR ASP THR PRO MET ALA SEQRES 15 A 366 ARG SER GLY LEU GLN TYR ASN SER LEU GLU GLU ILE HIS SEQRES 16 A 366 ILE PHE VAL LEU CYS ASN ILE LEU ARG ARG PRO ILE ILE SEQRES 17 A 366 VAL ILE SER ASP LYS MET LEU ARG SER LEU GLU SER GLY SEQRES 18 A 366 SER ASN PHE ALA PRO LEU LYS VAL GLY GLY ILE TYR LEU SEQRES 19 A 366 PRO LEU HIS TRP PRO ALA GLN GLU CYS TYR ARG TYR PRO SEQRES 20 A 366 ILE VAL LEU GLY TYR ASP SER HIS HIS PHE VAL PRO LEU SEQRES 21 A 366 VAL THR LEU LYS ASP SER GLY PRO GLU ILE ARG ALA VAL SEQRES 22 A 366 PRO LEU VAL ASN ARG ASP ARG GLY ARG PHE GLU ASP LEU SEQRES 23 A 366 LYS VAL HIS PHE LEU THR ASP PRO GLU ASN GLU MET LYS SEQRES 24 A 366 GLU LYS LEU LEU LYS GLU TYR LEU MET VAL ILE GLU ILE SEQRES 25 A 366 PRO VAL GLN GLY TRP ASP HIS GLY THR THR HIS LEU ILE SEQRES 26 A 366 ASN ALA ALA LYS LEU ASP GLU ALA ASN LEU PRO LYS GLU SEQRES 27 A 366 ILE ASN LEU VAL ASP ASP TYR PHE GLU LEU VAL GLN HIS SEQRES 28 A 366 GLU TYR LYS LYS TRP GLN GLU ASN SER GLU GLN GLY ARG SEQRES 29 A 366 ARG GLU SEQRES 1 B 366 MET ALA GLU GLN VAL LEU PRO GLN ALA LEU TYR LEU SER SEQRES 2 B 366 ASN MET ARG LYS ALA VAL LYS ILE ARG GLU ARG THR PRO SEQRES 3 B 366 GLU ASP ILE PHE LYS PRO THR ASN GLY ILE ILE HIS HIS SEQRES 4 B 366 PHE LYS THR MET HIS ARG TYR THR LEU GLU MET PHE ARG SEQRES 5 B 366 THR CYS GLN PHE CYS PRO GLN PHE ARG GLU ILE ILE HIS SEQRES 6 B 366 LYS ALA LEU ILE ASP ARG ASN ILE GLN ALA THR LEU GLU SEQRES 7 B 366 SER GLN LYS LYS LEU ASN TRP CYS ARG GLU VAL ARG LYS SEQRES 8 B 366 LEU VAL ALA LEU LYS THR ASN GLY ASP GLY ASN OCS LEU SEQRES 9 B 366 MET HIS ALA THR SER GLN TYR MET TRP SER VAL GLN ASP SEQRES 10 B 366 THR ASP LEU VAL LEU ARG LYS ALA LEU PHE SER THR LEU SEQRES 11 B 366 LYS GLU THR ASP THR ARG ASN PHE LYS PHE ARG TRP GLN SEQRES 12 B 366 LEU GLU SER LEU LYS SER GLN GLU PHE VAL GLU THR GLY SEQRES 13 B 366 LEU CYS TYR ASP THR ARG ASN TRP ASN ASP GLU TRP ASP SEQRES 14 B 366 ASN LEU ILE LYS MET ALA SER THR ASP THR PRO MET ALA SEQRES 15 B 366 ARG SER GLY LEU GLN TYR ASN SER LEU GLU GLU ILE HIS SEQRES 16 B 366 ILE PHE VAL LEU CYS ASN ILE LEU ARG ARG PRO ILE ILE SEQRES 17 B 366 VAL ILE SER ASP LYS MET LEU ARG SER LEU GLU SER GLY SEQRES 18 B 366 SER ASN PHE ALA PRO LEU LYS VAL GLY GLY ILE TYR LEU SEQRES 19 B 366 PRO LEU HIS TRP PRO ALA GLN GLU CYS TYR ARG TYR PRO SEQRES 20 B 366 ILE VAL LEU GLY TYR ASP SER HIS HIS PHE VAL PRO LEU SEQRES 21 B 366 VAL THR LEU LYS ASP SER GLY PRO GLU ILE ARG ALA VAL SEQRES 22 B 366 PRO LEU VAL ASN ARG ASP ARG GLY ARG PHE GLU ASP LEU SEQRES 23 B 366 LYS VAL HIS PHE LEU THR ASP PRO GLU ASN GLU MET LYS SEQRES 24 B 366 GLU LYS LEU LEU LYS GLU TYR LEU MET VAL ILE GLU ILE SEQRES 25 B 366 PRO VAL GLN GLY TRP ASP HIS GLY THR THR HIS LEU ILE SEQRES 26 B 366 ASN ALA ALA LYS LEU ASP GLU ALA ASN LEU PRO LYS GLU SEQRES 27 B 366 ILE ASN LEU VAL ASP ASP TYR PHE GLU LEU VAL GLN HIS SEQRES 28 B 366 GLU TYR LYS LYS TRP GLN GLU ASN SER GLU GLN GLY ARG SEQRES 29 B 366 ARG GLU MODRES 3ZJF CSD A 103 CYS 3-SULFINOALANINE MODRES 3ZJF OCS B 103 CYS CYSTEINE SULFONIC ACID HET CSD A 103 8 HET OCS B 103 9 HET CL B1357 1 HET CL B1358 1 HETNAM CL CHLORIDE ION HETNAM CSD 3-SULFINOALANINE HETNAM OCS CYSTEINESULFONIC ACID HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 3 CL 2(CL 1-) FORMUL 4 CSD C3 H7 N O4 S FORMUL 5 OCS C3 H7 N O5 S FORMUL 6 HOH *133(H2 O) HELIX 1 1 ALA A 9 SER A 13 5 5 HELIX 2 2 ASN A 14 THR A 25 1 12 HELIX 3 3 THR A 42 TYR A 46 5 5 HELIX 4 4 CYS A 57 ILE A 69 1 13 HELIX 5 5 ASP A 70 GLN A 80 1 11 HELIX 6 6 ASN A 102 SER A 114 1 13 HELIX 7 7 LEU A 120 THR A 133 1 14 HELIX 8 8 THR A 135 SER A 149 1 15 HELIX 9 9 ASN A 163 SER A 176 1 14 HELIX 10 10 GLU A 192 ARG A 204 1 13 HELIX 11 11 PRO A 239 CYS A 243 5 5 HELIX 12 12 THR A 292 MET A 298 1 7 HELIX 13 13 MET A 298 LEU A 307 1 10 HELIX 14 14 PRO A 336 ILE A 339 5 4 HELIX 15 15 ASN A 340 LYS A 355 1 16 HELIX 16 16 LEU B 10 SER B 13 5 4 HELIX 17 17 ASN B 14 ASP B 28 1 15 HELIX 18 18 THR B 42 TYR B 46 5 5 HELIX 19 19 CYS B 57 ILE B 69 1 13 HELIX 20 20 ASP B 70 GLN B 80 1 11 HELIX 21 21 ASN B 102 SER B 114 1 13 HELIX 22 22 LEU B 120 THR B 133 1 14 HELIX 23 23 THR B 135 LEU B 147 1 13 HELIX 24 24 ASN B 163 ALA B 175 1 13 HELIX 25 25 GLU B 192 ARG B 204 1 13 HELIX 26 26 PRO B 239 CYS B 243 5 5 HELIX 27 27 THR B 292 GLU B 297 1 6 HELIX 28 28 MET B 298 LEU B 307 1 10 HELIX 29 29 PRO B 336 ILE B 339 5 4 HELIX 30 30 ASN B 340 LYS B 355 1 16 SHEET 1 AA 2 ILE A 29 PHE A 30 0 SHEET 2 AA 2 HIS A 39 PHE A 40 -1 O HIS A 39 N PHE A 30 SHEET 1 AB 2 GLU A 49 MET A 50 0 SHEET 2 AB 2 HIS A 256 LEU A 263 1 O THR A 262 N MET A 50 SHEET 1 AC 2 LEU A 92 ALA A 94 0 SHEET 2 AC 2 HIS A 256 LEU A 263 -1 O VAL A 261 N VAL A 93 SHEET 1 AD 5 GLY A 231 TYR A 233 0 SHEET 2 AD 5 ILE A 207 SER A 211 -1 O ILE A 207 N TYR A 233 SHEET 3 AD 5 ILE A 248 ASP A 253 1 O ILE A 248 N ILE A 208 SHEET 4 AD 5 HIS A 256 LEU A 263 -1 O HIS A 256 N ASP A 253 SHEET 5 AD 5 LEU A 92 ALA A 94 -1 O VAL A 93 N VAL A 261 SHEET 1 AE 5 GLY A 231 TYR A 233 0 SHEET 2 AE 5 ILE A 207 SER A 211 -1 O ILE A 207 N TYR A 233 SHEET 3 AE 5 ILE A 248 ASP A 253 1 O ILE A 248 N ILE A 208 SHEET 4 AE 5 HIS A 256 LEU A 263 -1 O HIS A 256 N ASP A 253 SHEET 5 AE 5 GLU A 49 MET A 50 1 N MET A 50 O THR A 262 SHEET 1 AF 3 ALA A 272 PRO A 274 0 SHEET 2 AF 3 HIS A 323 LYS A 329 -1 O ALA A 328 N VAL A 273 SHEET 3 AF 3 VAL A 309 VAL A 314 -1 O ILE A 310 N ALA A 327 SHEET 1 AG 2 VAL A 276 ASP A 279 0 SHEET 2 AG 2 ARG A 282 ASP A 285 -1 O ARG A 282 N ASP A 279 SHEET 1 BA 2 ILE B 29 PHE B 30 0 SHEET 2 BA 2 HIS B 39 PHE B 40 -1 O HIS B 39 N PHE B 30 SHEET 1 BB 5 LEU B 92 ALA B 94 0 SHEET 2 BB 5 HIS B 256 THR B 262 -1 O VAL B 261 N VAL B 93 SHEET 3 BB 5 ILE B 248 ASP B 253 -1 O VAL B 249 N LEU B 260 SHEET 4 BB 5 ILE B 207 SER B 211 1 O ILE B 208 N LEU B 250 SHEET 5 BB 5 GLY B 231 TYR B 233 -1 O GLY B 231 N VAL B 209 SHEET 1 BC 3 ALA B 272 PRO B 274 0 SHEET 2 BC 3 THR B 322 LYS B 329 -1 O ALA B 328 N VAL B 273 SHEET 3 BC 3 VAL B 309 GLN B 315 -1 O ILE B 310 N ALA B 327 SHEET 1 BD 2 VAL B 276 ASP B 279 0 SHEET 2 BD 2 ARG B 282 ASP B 285 -1 O ARG B 282 N ASP B 279 LINK C ASN A 102 N CSD A 103 1555 1555 1.32 LINK C CSD A 103 N LEU A 104 1555 1555 1.33 LINK C ASN B 102 N OCS B 103 1555 1555 1.33 LINK C OCS B 103 N LEU B 104 1555 1555 1.33 CISPEP 1 SER A 266 GLY A 267 0 -8.95 CISPEP 2 GLY A 267 PRO A 268 0 -8.00 CISPEP 3 GLY B 267 PRO B 268 0 3.12 SITE 1 AC1 3 GLU A 311 GLY B 281 TRP B 317 SITE 1 AC2 4 CYS B 86 ARG B 87 ARG B 278 HOH B2021 CRYST1 43.700 68.800 85.000 98.44 100.56 97.04 P 1 1 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 0.022883 0.002826 0.004829 0.00000 SCALE2 0.000000 0.014645 0.002579 0.00000 SCALE3 0.000000 0.000000 0.012152 0.00000 MASTER 474 0 4 30 33 0 2 6 0 0 0 58 END