HEADER HYDROLASE 17-JAN-13 3ZJD TITLE A20 OTU DOMAIN IN REDUCED, ACTIVE STATE AT 1.87 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: A20P50; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OTU DOMAIN, RESIDUES 1-366; COMPND 5 SYNONYM: TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3, TNF ALPHA- COMPND 6 INDUCED PROTEIN 3, OTU DOMAIN-CONTAINING PROTEIN 7C, PUTATIVE DNA- COMPND 7 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 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 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 20-DEC-23 3ZJD 1 REMARK REVDAT 2 20-MAR-13 3ZJD 1 JRNL REVDAT 1 06-MAR-13 3ZJD 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 ESSN 2041-1723 JRNL PMID 23463012 JRNL DOI 10.1038/NCOMMS2567 REMARK 2 REMARK 2 RESOLUTION. 1.87 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 73777 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3706 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 34.2980 - 5.5324 0.88 2498 132 0.2216 0.2359 REMARK 3 2 5.5324 - 4.3942 0.86 2451 133 0.1637 0.1941 REMARK 3 3 4.3942 - 3.8396 0.92 2626 140 0.1533 0.1924 REMARK 3 4 3.8396 - 3.4889 0.94 2689 143 0.1643 0.1949 REMARK 3 5 3.4889 - 3.2390 0.95 2731 137 0.1731 0.2175 REMARK 3 6 3.2390 - 3.0482 0.95 2706 142 0.1923 0.2143 REMARK 3 7 3.0482 - 2.8956 0.95 2699 161 0.1850 0.2138 REMARK 3 8 2.8956 - 2.7696 0.96 2734 143 0.1934 0.2485 REMARK 3 9 2.7696 - 2.6630 0.95 2729 140 0.1860 0.2249 REMARK 3 10 2.6630 - 2.5712 0.96 2714 145 0.1882 0.1790 REMARK 3 11 2.5712 - 2.4908 0.96 2728 162 0.1791 0.2567 REMARK 3 12 2.4908 - 2.4196 0.96 2753 149 0.1811 0.2437 REMARK 3 13 2.4196 - 2.3559 0.95 2749 149 0.1759 0.2000 REMARK 3 14 2.3559 - 2.2985 0.95 2667 135 0.1700 0.2187 REMARK 3 15 2.2985 - 2.2462 0.96 2800 137 0.1754 0.1727 REMARK 3 16 2.2462 - 2.1984 0.96 2688 136 0.1715 0.2178 REMARK 3 17 2.1984 - 2.1545 0.96 2761 132 0.1781 0.2534 REMARK 3 18 2.1545 - 2.1138 0.96 2749 157 0.1845 0.2514 REMARK 3 19 2.1138 - 2.0761 0.95 2666 132 0.1894 0.2151 REMARK 3 20 2.0761 - 2.0409 0.96 2786 147 0.1878 0.2456 REMARK 3 21 2.0409 - 2.0080 0.95 2712 132 0.1957 0.2311 REMARK 3 22 2.0080 - 1.9771 0.95 2703 154 0.2083 0.2555 REMARK 3 23 1.9771 - 1.9480 0.95 2759 143 0.2114 0.2299 REMARK 3 24 1.9480 - 1.9206 0.95 2675 148 0.2143 0.2416 REMARK 3 25 1.9206 - 1.8946 0.95 2758 140 0.2390 0.2509 REMARK 3 26 1.8946 - 1.8700 0.90 2540 137 0.2438 0.3045 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.57 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 : 0.019 5392 REMARK 3 ANGLE : 1.755 7331 REMARK 3 CHIRALITY : 0.146 829 REMARK 3 PLANARITY : 0.008 929 REMARK 3 DIHEDRAL : 15.722 1985 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): -18.6407 25.9576 -12.1141 REMARK 3 T TENSOR REMARK 3 T11: 0.1423 T22: 0.1853 REMARK 3 T33: 0.1799 T12: -0.0349 REMARK 3 T13: -0.0154 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 2.1305 L22: 2.3127 REMARK 3 L33: 3.5044 L12: 0.1748 REMARK 3 L13: 0.3251 L23: -0.5986 REMARK 3 S TENSOR REMARK 3 S11: 0.0798 S12: -0.1235 S13: -0.0136 REMARK 3 S21: 0.3025 S22: -0.0338 S23: -0.1182 REMARK 3 S31: 0.1022 S32: -0.1611 S33: -0.0497 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -12.4083 38.1150 36.9036 REMARK 3 T TENSOR REMARK 3 T11: 0.2437 T22: 0.1802 REMARK 3 T33: 0.1999 T12: 0.0478 REMARK 3 T13: 0.0357 T23: -0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.5978 L22: 2.7939 REMARK 3 L33: 2.6147 L12: -0.0667 REMARK 3 L13: 0.2223 L23: -0.8170 REMARK 3 S TENSOR REMARK 3 S11: 0.0698 S12: 0.0545 S13: 0.1550 REMARK 3 S21: -0.5308 S22: -0.1202 S23: -0.0648 REMARK 3 S31: -0.1607 S32: 0.0702 S33: 0.0257 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 WERE REMARK 3 NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE MISSING REMARK 3 FROM THE STRUCTURE. SEVERAL RESIDUES WERE MODELLED WITH REMARK 3 OCCUPANCY SET TO 0 OR WITH SIDE CHAINS REMOVED. REMARK 4 REMARK 4 3ZJD 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 DEPOSITION ID IS D_1290055467. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-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) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73826 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 47.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-2.5 M NACL, 0.1 M MES [PH 6-6.7], 10 REMARK 280 MM DTT., PH 6.2 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: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.3 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 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 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 SER A 266 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 ASN B 163 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 LEU B 227 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 VAL A 5 CG1 CG2 REMARK 470 LEU A 6 CG CD1 CD2 REMARK 470 LYS A 31 CG CD CE NZ REMARK 470 THR A 33 OG1 CG2 REMARK 470 GLN A 55 CG CD OE1 NE2 REMARK 470 GLN A 59 CG CD OE1 NE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 GLU A 88 CG CD OE1 OE2 REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 SER A 149 OG REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 LEU A 227 CG CD1 CD2 REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 264 CD CE NZ REMARK 470 ASP A 265 CG OD1 OD2 REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 THR A 321 OG1 CG2 REMARK 470 GLU A 332 CG CD OE1 OE2 REMARK 470 LYS A 337 CG CD CE NZ 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 REMARK 470 TRP A 356 CZ3 CH2 REMARK 470 GLN B 8 CG CD OE1 NE2 REMARK 470 TYR B 11 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 27 CG CD OE1 OE2 REMARK 470 THR B 33 OG1 CG2 REMARK 470 GLN B 55 CG CD OE1 NE2 REMARK 470 GLN B 59 CG CD OE1 NE2 REMARK 470 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 GLU B 132 CG CD OE1 OE2 REMARK 470 THR B 133 OG1 CG2 REMARK 470 ASP B 134 CG OD1 OD2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 ASP B 169 CB CG OD1 OD2 REMARK 470 THR B 179 OG1 CG2 REMARK 470 LYS B 228 CG CD CE NZ 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 GLU B 297 CG CD OE1 OE2 REMARK 470 LYS B 337 CG CD CE NZ REMARK 470 GLU B 338 CG CD OE1 OE2 REMARK 470 ASN B 340 CG OD1 ND2 REMARK 470 GLU B 347 CG CD OE1 OE2 REMARK 470 LYS B 354 CG CD CE NZ REMARK 470 LYS B 355 CG CD CE NZ REMARK 470 TRP B 356 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 356 CZ3 CH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG B 282 CD NE CZ NH1 NH2 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 HOH A 2120 O HOH A 2121 1.98 REMARK 500 OG1 THR B 53 NE2 HIS B 65 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 293 NZ LYS B 139 1444 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 86 CB CYS A 86 SG -0.121 REMARK 500 CYS A 86 CB CYS A 86 SG -0.131 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 318 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES 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 80.79 -159.30 REMARK 500 THR A 42 -34.30 -146.40 REMARK 500 ARG A 280 -126.34 52.56 REMARK 500 ASP A 318 -78.91 -113.95 REMARK 500 THR A 321 -117.61 47.48 REMARK 500 GLU A 338 -35.10 -33.74 REMARK 500 LYS A 355 2.66 -66.05 REMARK 500 PRO B 7 152.32 -49.59 REMARK 500 ASN B 14 82.18 -163.29 REMARK 500 THR B 42 -32.08 -141.23 REMARK 500 ASP B 117 47.94 -91.33 REMARK 500 GLU B 132 -70.51 -125.20 REMARK 500 THR B 133 -177.21 -50.45 REMARK 500 PRO B 336 -178.66 -59.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 321 THR A 322 -141.68 REMARK 500 ASN B 165 ASP B 166 147.89 REMARK 500 SER B 266 GLY B 267 147.59 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 B 1358 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1359 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1357 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1358 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZJE RELATED DB: PDB REMARK 900 A20 OTU DOMAIN IN REVERSIBLY OXIDISED (SOH) STATE REMARK 900 RELATED ID: 3ZJF RELATED DB: PDB REMARK 900 A20 OTU DOMAIN WITH IRREVERSIBLY OXIDISED CYS103 FROM 270 MIN H2O2 REMARK 900 SOAK. REMARK 900 RELATED ID: 3ZJG RELATED DB: PDB REMARK 900 A20 OTU DOMAIN WITH IRREVERSIBLY OXIDISED CYS103 FROM 60 MIN H2O2 REMARK 900 SOAK. DBREF 3ZJD A 1 366 UNP P21580 TNAP3_HUMAN 1 366 DBREF 3ZJD B 1 366 UNP P21580 TNAP3_HUMAN 1 366 SEQADV 3ZJD SER A 114 UNP P21580 GLY 114 ENGINEERED MUTATION SEQADV 3ZJD 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 CYS 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 CYS 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 HET CL A1357 1 HET EDO A1358 4 HET CL B1358 1 HET CL B1359 1 HET CL B1360 1 HET CL B1361 1 HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CL 5(CL 1-) FORMUL 4 EDO C2 H6 O2 FORMUL 9 HOH *253(H2 O) HELIX 1 1 ALA A 9 SER A 13 5 5 HELIX 2 2 ASN A 14 ASP A 28 1 15 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 LYS A 148 1 14 HELIX 9 9 ASN A 163 ALA A 175 1 13 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 ALA B 9 SER B 13 5 5 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 GLU B 132 1 13 HELIX 23 23 THR B 135 LYS B 148 1 14 HELIX 24 24 ASP B 166 ALA B 175 1 10 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 ASN B 340 TRP B 356 1 17 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 5 LEU A 92 ALA A 94 0 SHEET 2 AB 5 HIS A 256 THR A 262 -1 O VAL A 261 N VAL A 93 SHEET 3 AB 5 ILE A 248 ASP A 253 -1 O VAL A 249 N LEU A 260 SHEET 4 AB 5 ILE A 207 SER A 211 1 O ILE A 208 N LEU A 250 SHEET 5 AB 5 GLY A 231 TYR A 233 -1 O GLY A 231 N VAL A 209 SHEET 1 AC 3 ALA A 272 PRO A 274 0 SHEET 2 AC 3 THR A 322 LYS A 329 -1 O ALA A 328 N VAL A 273 SHEET 3 AC 3 VAL A 309 GLN A 315 -1 O ILE A 310 N ALA A 327 SHEET 1 AD 2 VAL A 276 ASP A 279 0 SHEET 2 AD 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 CISPEP 1 GLY A 267 PRO A 268 0 -0.53 CISPEP 2 GLY B 267 PRO B 268 0 5.60 SITE 1 AC1 4 CYS B 86 ARG B 87 ARG B 278 HOH B2039 SITE 1 AC2 3 GLU A 311 GLY B 281 TRP B 317 SITE 1 AC3 4 MET A 308 TRP B 317 ASP B 318 HIS B 323 SITE 1 AC4 4 GLY A 230 GLY A 231 LYS A 287 HOH A2098 SITE 1 AC5 4 ARG B 45 CYS B 243 TYR B 244 HOH B2016 SITE 1 AC6 8 LEU A 275 ASP A 285 LEU A 286 LYS A 299 SITE 2 AC6 8 GLU A 300 LEU A 303 ASN A 326 HOH A2119 CRYST1 43.690 68.970 84.300 99.04 100.09 96.95 P 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 0.022889 0.002790 0.004660 0.00000 SCALE2 0.000000 0.014606 0.002711 0.00000 SCALE3 0.000000 0.000000 0.012254 0.00000