HEADER HYDROLASE REGULATOR 25-JUN-13 4LDT TITLE THE STRUCTURE OF H/CEOTUB1-UBIQUITIN ALDEHYDE-UBCH5B~UB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN THIOESTERASE OTUBAIN-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME OTUB1, OTU DOMAIN-CONTAINING COMPND 6 UBIQUITIN ALDEHYDE-BINDING PROTEIN 1, OTUBAIN-1, HOTU1, UBIQUITIN- COMPND 7 SPECIFIC-PROCESSING PROTEASE OTUB1, DEUBIQUITINATING ENZYME OTUBAIN- COMPND 8 LIKE, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE OTUBAIN-LIKE; COMPND 9 EC: 3.4.19.12; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN ALDEHYDE; COMPND 13 CHAIN: B; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: UBIQUITIN CARRIER PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME COMPND 19 E2(17)KB 2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, UBIQUITIN- COMPND 20 PROTEIN LIGASE D2, P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1; COMPND 21 EC: 6.3.2.19; COMPND 22 ENGINEERED: YES; COMPND 23 MUTATION: YES; COMPND 24 MOL_ID: 4; COMPND 25 MOLECULE: UBIQUITIN; COMPND 26 CHAIN: D; COMPND 27 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: HUMAN, NEMATODE; SOURCE 4 ORGANISM_TAXID: 9606, 6239; SOURCE 5 GENE: OTUB1, OTB1, OTU1, HSPC263, C25D7.8, OTUB-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBC; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 GENE: UBC; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOPEPTIDASE, UBIQUITIN-CONJUGATING, POST-TRANSLATIONAL MODIFICATION, KEYWDS 2 UBIQUITIN, UBIQUITIN-ALDEHYDE, HYDROLASE REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR R.WIENER,A.T.DIBELLO,P.M.LOMBARDI,C.M.GUZZO,X.ZHANG,M.J.MATUNIS, AUTHOR 2 C.WOLBERGER REVDAT 6 06-DEC-23 4LDT 1 REMARK REVDAT 5 20-SEP-23 4LDT 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 4LDT 1 SOURCE REMARK REVDAT 3 25-SEP-13 4LDT 1 JRNL REVDAT 2 04-SEP-13 4LDT 1 JRNL REVDAT 1 14-AUG-13 4LDT 0 JRNL AUTH R.WIENER,A.T.DIBELLO,P.M.LOMBARDI,C.M.GUZZO,X.ZHANG, JRNL AUTH 2 M.J.MATUNIS,C.WOLBERGER JRNL TITL E2 UBIQUITIN-CONJUGATING ENZYMES REGULATE THE JRNL TITL 2 DEUBIQUITINATING ACTIVITY OF OTUB1. JRNL REF NAT.STRUCT.MOL.BIOL. V. 20 1033 2013 JRNL REFN ISSN 1545-9993 JRNL PMID 23955022 JRNL DOI 10.1038/NSMB.2655 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 48379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2612 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3360 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4362 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 316 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : -2.07000 REMARK 3 B33 (A**2) : 1.71000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.665 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4626 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4400 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6299 ; 1.248 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10122 ; 0.741 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 5.591 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;32.043 ;23.578 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 783 ;13.643 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;14.683 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 707 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5282 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1067 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 19 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4888 27.6598 15.7155 REMARK 3 T TENSOR REMARK 3 T11: 0.0810 T22: 0.1344 REMARK 3 T33: 0.0131 T12: -0.0320 REMARK 3 T13: 0.0157 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.7276 L22: 0.8361 REMARK 3 L33: 0.6596 L12: 0.2420 REMARK 3 L13: 0.0843 L23: 0.2154 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: -0.0587 S13: 0.0211 REMARK 3 S21: 0.0293 S22: -0.0318 S23: 0.0927 REMARK 3 S31: -0.0427 S32: -0.0576 S33: 0.0341 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): 33.4698 43.7505 -0.2706 REMARK 3 T TENSOR REMARK 3 T11: 0.1114 T22: 0.1180 REMARK 3 T33: 0.0096 T12: -0.0378 REMARK 3 T13: 0.0005 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.1765 L22: 1.8178 REMARK 3 L33: 1.3228 L12: 1.0693 REMARK 3 L13: -0.2282 L23: -0.1895 REMARK 3 S TENSOR REMARK 3 S11: 0.0144 S12: 0.0457 S13: 0.0595 REMARK 3 S21: -0.1300 S22: 0.0659 S23: 0.0884 REMARK 3 S31: -0.0373 S32: 0.0640 S33: -0.0803 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 0 C 147 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1611 1.4996 -6.7362 REMARK 3 T TENSOR REMARK 3 T11: 0.0590 T22: 0.0868 REMARK 3 T33: 0.0155 T12: -0.0288 REMARK 3 T13: 0.0078 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.1624 L22: 1.2586 REMARK 3 L33: 2.3610 L12: -0.1119 REMARK 3 L13: -0.6866 L23: 0.5419 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: 0.0289 S13: 0.0470 REMARK 3 S21: -0.1395 S22: -0.0337 S23: -0.0572 REMARK 3 S31: 0.0032 S32: 0.1618 S33: 0.0602 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 76 REMARK 3 ORIGIN FOR THE GROUP (A): 41.2208 18.2454 10.6816 REMARK 3 T TENSOR REMARK 3 T11: 0.0668 T22: 0.2393 REMARK 3 T33: 0.2089 T12: 0.0404 REMARK 3 T13: -0.0057 T23: -0.1006 REMARK 3 L TENSOR REMARK 3 L11: 0.7761 L22: 3.8638 REMARK 3 L33: 3.1631 L12: 1.3510 REMARK 3 L13: -0.1426 L23: 1.8496 REMARK 3 S TENSOR REMARK 3 S11: -0.0730 S12: 0.0156 S13: -0.3091 REMARK 3 S21: 0.0933 S22: 0.4084 S23: -0.8059 REMARK 3 S31: 0.2319 S32: 0.4830 S33: -0.3354 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4LDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080503. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.901 REMARK 200 RESOLUTION RANGE LOW (A) : 33.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13000 REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57000 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.7.0029 REMARK 200 STARTING MODEL: PDB ENTRY 4DHZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 MIX OF 12 MG/ML PURIFIED COMPLEX REMARK 280 AND WELL SOLUTION (100 MM BIS-TRIS, PH 6.0, 200 MM MAGNESIUM REMARK 280 CHLORIDE, 22% PEG3350), CRYSTALS APPEARED IN ABOUT 2 TO 3 DAYS, REMARK 280 CRYOPROTECTION WITH WELL SOLUTION + 10% ETHYLENE GLYCOL, FLASH REMARK 280 FROZEN IN LIQUID NITROGEN, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 52.44700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.80600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 52.44700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 65.80600 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -3 REMARK 465 ALA A -2 REMARK 465 ALA A -1 REMARK 465 GLU A 0 REMARK 465 GLU A 1 REMARK 465 PRO A 2 REMARK 465 GLN A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 LYS A 6 REMARK 465 GLN A 7 REMARK 465 GLU A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 ASP A 13 REMARK 465 SER A 14 REMARK 465 GLU A 15 REMARK 465 GLY A 16 REMARK 465 VAL A 17 REMARK 465 ASN A 18 REMARK 465 ASP A 252 REMARK 465 GLN A 253 REMARK 465 SER A 276 REMARK 465 THR A 277 REMARK 465 GLU A 278 REMARK 465 ALA A 279 REMARK 465 SER A 280 REMARK 465 GLU A 281 REMARK 465 ILE A 282 REMARK 465 GLU A 283 REMARK 465 ASN A 284 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 GLU A 124 CG CD OE1 OE2 REMARK 470 ASP A 129 CG OD1 OD2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 GLN A 254 CG CD OE1 NE2 REMARK 470 ILE A 255 CG1 CG2 CD1 REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ASP C 28 CG OD1 OD2 REMARK 470 ASP C 42 CG OD1 OD2 REMARK 470 ASP C 87 CG OD1 OD2 REMARK 470 ASP C 116 CG OD1 OD2 REMARK 470 GLU C 122 CG CD OE1 OE2 REMARK 470 LYS C 128 CG CD CE NZ REMARK 470 GLU C 132 CG CD OE1 OE2 REMARK 470 GLN D 2 CG CD OE1 NE2 REMARK 470 GLU D 16 CG CD OE1 OE2 REMARK 470 GLU D 24 CG CD OE1 OE2 REMARK 470 LYS D 63 CG CD CE NZ REMARK 470 GLU D 64 CG CD OE1 OE2 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 D 113 O HOH D 120 2.07 REMARK 500 O HOH A 541 O HOH C 374 2.18 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 TYR A 22 -73.21 -54.27 REMARK 500 SER A 62 49.54 -146.70 REMARK 500 ASP A 235 -166.53 -111.79 REMARK 500 ASP C 16 64.97 -153.67 REMARK 500 GLN C 20 -1.60 79.87 REMARK 500 ARG C 90 -89.42 -138.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 32 OD1 REMARK 620 2 HOH B 220 O 148.8 REMARK 620 3 HOH B 221 O 82.7 122.4 REMARK 620 4 HOH B 222 O 84.5 80.1 85.2 REMARK 620 5 HOH B 227 O 76.0 78.2 158.6 93.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 201 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING REMARK 999 RESIDUES 1-45 OF UNP Q96FW1 AND RESIDUES 42-284 OF UNP Q9XVR6. DBREF 4LDT A -3 41 UNP Q96FW1 OTUB1_HUMAN 1 45 DBREF 4LDT A 42 284 UNP Q9XVR6 OTUBL_CAEEL 42 284 DBREF 4LDT B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4LDT C 1 147 UNP P62837 UB2D2_HUMAN 1 147 DBREF 4LDT D 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 4LDT GLY C 0 UNP P62837 EXPRESSION TAG SEQADV 4LDT SER C 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQRES 1 A 288 MET ALA ALA GLU GLU PRO GLN GLN GLN LYS GLN GLU PRO SEQRES 2 A 288 LEU GLY SER ASP SER GLU GLY VAL ASN CYS LEU ALA TYR SEQRES 3 A 288 ASP GLU ALA ILE MET ALA GLN GLN ASP ARG ILE GLN GLN SEQRES 4 A 288 GLU ILE ALA VAL GLN ASN PRO LEU VAL ALA THR LEU ALA SEQRES 5 A 288 PRO PHE SER ILE LEU CYS ALA GLU TYR ASP ASN GLU THR SEQRES 6 A 288 SER ALA ALA PHE LEU SER LYS ALA THR GLU LEU SER GLU SEQRES 7 A 288 VAL TYR GLY GLU ILE ARG TYR ILE ARG GLY ASP GLY ASN SEQRES 8 A 288 CYS PHE TYR ARG ALA ILE LEU VAL GLY LEU ILE GLU ILE SEQRES 9 A 288 MET LEU LYS ASP ARG ALA ARG LEU GLU LYS PHE ILE ALA SEQRES 10 A 288 SER SER ARG ASP TRP THR ARG THR LEU VAL GLU LEU GLY SEQRES 11 A 288 PHE PRO ASP TRP THR CYS THR ASP PHE CYS ASP PHE PHE SEQRES 12 A 288 ILE GLU PHE LEU GLU LYS ILE HIS SER GLY VAL HIS THR SEQRES 13 A 288 GLU GLU ALA VAL TYR THR ILE LEU ASN ASP ASP GLY SER SEQRES 14 A 288 ALA ASN TYR ILE LEU MET PHE PHE ARG LEU ILE THR SER SEQRES 15 A 288 ALA PHE LEU LYS GLN ASN SER GLU GLU TYR ALA PRO PHE SEQRES 16 A 288 ILE ASP GLU GLY MET THR VAL ALA GLN TYR CYS GLU GLN SEQRES 17 A 288 GLU ILE GLU PRO MET TRP LYS ASP ALA ASP HIS LEU ALA SEQRES 18 A 288 ILE ASN SER LEU ILE LYS ALA ALA GLY THR ARG VAL ARG SEQRES 19 A 288 ILE GLU TYR MET ASP ARG THR ALA ALA PRO ASN GLY GLY SEQRES 20 A 288 TRP HIS TYR ASP ILE PRO SER ASP ASP GLN GLN ILE ALA SEQRES 21 A 288 PRO GLU ILE THR LEU LEU TYR ARG PRO GLY HIS TYR ASP SEQRES 22 A 288 VAL ILE TYR LYS LYS ASP SER THR GLU ALA SER GLU ILE SEQRES 23 A 288 GLU ASN SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLZ SEQRES 1 C 148 GLY MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP SEQRES 2 C 148 LEU ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO SEQRES 3 C 148 VAL GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET SEQRES 4 C 148 GLY PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE SEQRES 5 C 148 LEU THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO SEQRES 6 C 148 PRO LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN SEQRES 7 C 148 ILE ASN SER ASN GLY SER ILE SER LEU ASP ILE LEU ARG SEQRES 8 C 148 SER GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU SEQRES 9 C 148 LEU SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP SEQRES 10 C 148 ASP PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR SEQRES 11 C 148 ASP ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR SEQRES 12 C 148 GLN LYS TYR ALA MET SEQRES 1 D 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MODRES 4LDT GLZ B 76 GLY AMINO-ACETALDEHYDE HET GLZ B 76 4 HET EDO A 301 4 HET EDO A 302 4 HET EDO A 303 4 HET MG B 101 1 HET EDO C 201 4 HETNAM GLZ AMINO-ACETALDEHYDE HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GLZ C2 H5 N O FORMUL 5 EDO 4(C2 H6 O2) FORMUL 8 MG MG 2+ FORMUL 10 HOH *316(H2 O) HELIX 1 1 CYS A 19 ASN A 41 1 23 HELIX 2 2 PHE A 50 GLU A 56 1 7 HELIX 3 3 SER A 62 SER A 73 1 12 HELIX 4 4 ASN A 87 ASP A 104 1 18 HELIX 5 5 ASP A 104 LEU A 125 1 22 HELIX 6 6 PRO A 128 SER A 148 1 21 HELIX 7 7 THR A 152 ASP A 162 1 11 HELIX 8 8 ASP A 162 ASN A 184 1 23 HELIX 9 9 ASN A 184 ALA A 189 1 6 HELIX 10 10 PRO A 190 ILE A 192 5 3 HELIX 11 11 THR A 197 ILE A 206 1 10 HELIX 12 12 ASP A 214 ALA A 225 1 12 HELIX 13 13 THR B 22 GLY B 35 1 14 HELIX 14 14 PRO B 37 ASP B 39 5 3 HELIX 15 15 MET C 1 ASP C 16 1 16 HELIX 16 16 LEU C 86 ARG C 90 5 5 HELIX 17 17 THR C 98 ASP C 112 1 15 HELIX 18 18 VAL C 120 ASP C 130 1 11 HELIX 19 19 ASP C 130 ALA C 146 1 17 HELIX 20 20 THR D 22 GLY D 35 1 14 HELIX 21 21 PRO D 37 ASP D 39 5 3 HELIX 22 22 LEU D 56 ASN D 60 5 5 SHEET 1 A 6 ALA A 48 PRO A 49 0 SHEET 2 A 6 TYR A 76 ARG A 80 -1 O ILE A 79 N ALA A 48 SHEET 3 A 6 HIS A 267 LYS A 273 -1 O VAL A 270 N ARG A 80 SHEET 4 A 6 ILE A 259 ARG A 264 -1 N ARG A 264 O HIS A 267 SHEET 5 A 6 VAL A 229 TYR A 233 1 N GLU A 232 O TYR A 263 SHEET 6 A 6 TRP A 244 ILE A 248 -1 O TYR A 246 N ILE A 231 SHEET 1 B 5 THR B 12 GLU B 16 0 SHEET 2 B 5 GLN B 2 THR B 7 -1 N ILE B 3 O LEU B 15 SHEET 3 B 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 B 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 B 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 C 4 CYS C 21 PRO C 25 0 SHEET 2 C 4 HIS C 32 MET C 38 -1 O GLN C 34 N GLY C 24 SHEET 3 C 4 VAL C 49 HIS C 55 -1 O PHE C 50 N ILE C 37 SHEET 4 C 4 LYS C 66 PHE C 69 -1 O LYS C 66 N HIS C 55 SHEET 1 D 5 THR D 12 GLU D 16 0 SHEET 2 D 5 GLN D 2 LYS D 6 -1 N VAL D 5 O ILE D 13 SHEET 3 D 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 D 5 GLN D 41 PHE D 45 -1 N ILE D 44 O HIS D 68 SHEET 5 D 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 LINK SG CYS A 88 C GLZ B 76 1555 1555 1.76 LINK C GLY B 75 N GLZ B 76 1555 1555 1.33 LINK OG SER C 85 C GLY D 76 1555 1555 1.44 LINK OD1 ASP B 32 MG MG B 101 1555 1555 2.23 LINK MG MG B 101 O HOH B 220 1555 1555 2.23 LINK MG MG B 101 O HOH B 221 1555 1555 2.25 LINK MG MG B 101 O HOH B 222 1555 1555 2.13 LINK MG MG B 101 O HOH B 227 1555 1555 2.18 CISPEP 1 ILE A 248 PRO A 249 0 -4.46 CISPEP 2 TYR C 60 PRO C 61 0 0.10 SITE 1 AC1 4 MET A 101 LEU A 102 ARG A 105 ILE A 146 SITE 1 AC2 3 ALA A 155 THR A 158 HOH A 492 SITE 1 AC3 8 ILE A 192 ASP A 193 GLU A 194 TYR A 201 SITE 2 AC3 8 ASP A 214 LEU A 216 HOH A 450 HOH A 482 SITE 1 AC4 5 ASP B 32 HOH B 220 HOH B 221 HOH B 222 SITE 2 AC4 5 HOH B 227 SITE 1 AC5 5 MET C 38 GLY C 39 GLN C 46 GLY C 47 SITE 2 AC5 5 GLY C 48 CRYST1 104.894 131.612 46.501 90.00 90.00 90.00 P 21 21 2 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 0.009533 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021505 0.00000