PDB Short entry for 4BOZ HEADER HYDROLASE 22-MAY-13 4BOZ TITLE STRUCTURE OF OTUD2 OTU DOMAIN IN COMPLEX WITH K11-LINKED DI UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN THIOESTERASE OTU1; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: RESIDUES 132-314; COMPND 5 SYNONYM: OTUD2, DUBA-8, HIV-1-INDUCED PROTEASE 7, HIN-7, HSHIN7, OTU COMPND 6 DOMAIN-CONTAINING PROTEIN 2; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: UBIQUITIN-C; COMPND 12 CHAIN: B, C, E; COMPND 13 SYNONYM: UBIQUITIN; COMPND 14 ENGINEERED: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLACI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: POPINK; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLACI; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PET17B KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.E.T.MEVISSEN,M.K.HOSPENTHAL,P.P.GEURINK,P.R.ELLIOTT,M.AKUTSU, AUTHOR 2 N.ARNAUDO,R.EKKEBUS,Y.KULATHU,T.WAUER,F.EL OUALID,S.M.V.FREUND, AUTHOR 3 H.OVAA,D.KOMANDER REVDAT 2 20-DEC-23 4BOZ 1 REMARK REVDAT 1 17-JUL-13 4BOZ 0 JRNL AUTH T.E.T.MEVISSEN,M.K.HOSPENTHAL,P.P.GEURINK,P.R.ELLIOTT, JRNL AUTH 2 M.AKUTSU,N.ARNAUDO,R.EKKEBUS,Y.KULATHU,T.WAUER,F.EL OUALID, JRNL AUTH 3 S.M.V.FREUND,H.OVAA,D.KOMANDER JRNL TITL OTU DEUBIQUITINASES REVEAL MECHANISMS OF LINKAGE SPECIFICITY JRNL TITL 2 AND ENABLE UBIQUITIN CHAIN RESTRICTION ANALYSIS. JRNL REF CELL(CAMBRIDGE,MASS.) V. 154 169 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23827681 JRNL DOI 10.1016/J.CELL.2013.05.046 REMARK 2 REMARK 2 RESOLUTION. 3.03 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) : 3.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 12689 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 613 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 43.6888 - 4.8082 0.97 3098 156 0.2120 0.2681 REMARK 3 2 4.8082 - 3.8172 0.97 2988 154 0.1635 0.2152 REMARK 3 3 3.8172 - 3.3348 0.98 2999 150 0.1883 0.2484 REMARK 3 4 3.3348 - 3.0300 0.98 2991 153 0.2257 0.3215 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.89 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 : 0.009 4317 REMARK 3 ANGLE : 1.156 5866 REMARK 3 CHIRALITY : 0.072 689 REMARK 3 PLANARITY : 0.005 764 REMARK 3 DIHEDRAL : 14.931 1598 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN C AND ((RESSEQ 1:71)) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4659 -10.8947 -50.1637 REMARK 3 T TENSOR REMARK 3 T11: 0.6816 T22: 0.6087 REMARK 3 T33: 0.4748 T12: 0.1079 REMARK 3 T13: 0.0564 T23: 0.1144 REMARK 3 L TENSOR REMARK 3 L11: 3.8521 L22: 4.2360 REMARK 3 L33: 5.2652 L12: 0.8850 REMARK 3 L13: 0.5010 L23: -0.2414 REMARK 3 S TENSOR REMARK 3 S11: 0.5627 S12: 0.8588 S13: 0.1377 REMARK 3 S21: 0.1419 S22: 0.3445 S23: 0.4554 REMARK 3 S31: -0.3421 S32: -0.0271 S33: -0.7974 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND ((RESSEQ 1:76)) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0282 -9.2844 -26.0052 REMARK 3 T TENSOR REMARK 3 T11: 0.5659 T22: 1.1244 REMARK 3 T33: 0.7789 T12: 0.0971 REMARK 3 T13: 0.2902 T23: 0.3344 REMARK 3 L TENSOR REMARK 3 L11: 3.0934 L22: 1.6932 REMARK 3 L33: 0.2238 L12: -1.3643 REMARK 3 L13: -0.5679 L23: 0.0041 REMARK 3 S TENSOR REMARK 3 S11: -0.0886 S12: 0.1458 S13: 0.1871 REMARK 3 S21: -0.6369 S22: -0.5451 S23: -1.2787 REMARK 3 S31: 0.2167 S32: 1.4288 S33: 0.4048 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN E AND ((RESSEQ 1:76)) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9134 -4.5424 11.5888 REMARK 3 T TENSOR REMARK 3 T11: 0.4038 T22: 0.5409 REMARK 3 T33: 0.4547 T12: -0.0160 REMARK 3 T13: -0.0753 T23: 0.1105 REMARK 3 L TENSOR REMARK 3 L11: 4.3094 L22: 2.3328 REMARK 3 L33: 2.4510 L12: -1.6518 REMARK 3 L13: 0.5816 L23: -0.9016 REMARK 3 S TENSOR REMARK 3 S11: 0.2112 S12: -1.1563 S13: -0.5705 REMARK 3 S21: 0.2945 S22: 0.0958 S23: -0.0164 REMARK 3 S31: 0.4010 S32: 0.3725 S33: -0.2422 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D AND ((RESSEQ 146:311)) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9730 11.5136 0.9821 REMARK 3 T TENSOR REMARK 3 T11: 0.2284 T22: 0.2608 REMARK 3 T33: 0.2712 T12: -0.0348 REMARK 3 T13: -0.0043 T23: 0.0548 REMARK 3 L TENSOR REMARK 3 L11: 3.1865 L22: 2.6042 REMARK 3 L33: 1.9612 L12: -0.6813 REMARK 3 L13: -0.7571 L23: 0.5798 REMARK 3 S TENSOR REMARK 3 S11: 0.2113 S12: -0.3109 S13: 0.3728 REMARK 3 S21: 0.0215 S22: -0.0149 S23: 0.0239 REMARK 3 S31: -0.0104 S32: -0.1315 S33: -0.1740 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND ((RESSEQ 147:308)) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5781 -12.7487 -20.3831 REMARK 3 T TENSOR REMARK 3 T11: 0.3453 T22: 0.2045 REMARK 3 T33: 0.2346 T12: 0.0035 REMARK 3 T13: -0.0402 T23: 0.0322 REMARK 3 L TENSOR REMARK 3 L11: 2.5634 L22: 3.1945 REMARK 3 L33: 3.0789 L12: -0.4497 REMARK 3 L13: 0.7449 L23: -0.3564 REMARK 3 S TENSOR REMARK 3 S11: 0.1580 S12: 0.1484 S13: -0.1672 REMARK 3 S21: -0.5364 S22: -0.0847 S23: 0.0875 REMARK 3 S31: 0.0470 S32: 0.0035 S33: -0.0349 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 4BOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12691 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.030 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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 4BOQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M POTASSIUM THIOCYANATE, 18% PEG REMARK 280 5K MME, 0.1 M SODIUM ACETATE PH 5.5 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 87.39500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 87.39500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.11000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.4 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 350 REMARK 350 BIOMOLECULE: 2 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: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 ALA A 132 REMARK 465 PHE A 133 REMARK 465 THR A 134 REMARK 465 LYS A 135 REMARK 465 ARG A 136 REMARK 465 GLY A 137 REMARK 465 ALA A 138 REMARK 465 SER A 139 REMARK 465 SER A 140 REMARK 465 TYR A 141 REMARK 465 VAL A 142 REMARK 465 ARG A 143 REMARK 465 GLU A 144 REMARK 465 THR A 145 REMARK 465 LEU A 146 REMARK 465 PRO A 276 REMARK 465 ASP A 277 REMARK 465 PRO A 278 REMARK 465 ASP A 279 REMARK 465 GLN A 309 REMARK 465 PHE A 310 REMARK 465 THR A 311 REMARK 465 ASP A 312 REMARK 465 VAL A 313 REMARK 465 ASN A 314 REMARK 465 ARG C 72 REMARK 465 LEU C 73 REMARK 465 ARG C 74 REMARK 465 GLY C 75 REMARK 465 GLY C 76 REMARK 465 ALA D 132 REMARK 465 PHE D 133 REMARK 465 THR D 134 REMARK 465 LYS D 135 REMARK 465 ARG D 136 REMARK 465 GLY D 137 REMARK 465 ALA D 138 REMARK 465 SER D 139 REMARK 465 SER D 140 REMARK 465 TYR D 141 REMARK 465 VAL D 142 REMARK 465 ARG D 143 REMARK 465 GLU D 144 REMARK 465 THR D 145 REMARK 465 LEU D 146 REMARK 465 ASP D 312 REMARK 465 VAL D 313 REMARK 465 ASN D 314 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 199 CG CD OE1 OE2 REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 GLN A 242 CG CD OE1 NE2 REMARK 470 ASP A 252 CG OD1 OD2 REMARK 470 LYS A 257 CG CD CE NZ REMARK 470 GLU A 303 CD OE1 OE2 REMARK 470 ARG A 305 CD NE CZ NH1 NH2 REMARK 470 ARG A 307 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 308 CG CD NE CZ NH1 NH2 REMARK 470 MET B 1 CG SD CE REMARK 470 GLN B 2 CG CD OE1 NE2 REMARK 470 PHE B 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 THR B 12 OG1 CG2 REMARK 470 ILE B 13 CG1 CG2 CD1 REMARK 470 GLU B 16 CG CD OE1 OE2 REMARK 470 VAL B 17 CG1 CG2 REMARK 470 GLU B 18 CG CD OE1 OE2 REMARK 470 ILE B 23 CG1 CG2 CD1 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ASN B 25 CG OD1 ND2 REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 ASP B 32 CG OD1 OD2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 ASP B 39 CG OD1 OD2 REMARK 470 PHE B 45 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 GLU B 51 CG CD OE1 OE2 REMARK 470 ASP B 52 CG OD1 OD2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 56 CG CD1 CD2 REMARK 470 SER B 57 OG REMARK 470 TYR B 59 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN B 60 CG OD1 ND2 REMARK 470 GLN B 62 CG CD OE1 NE2 REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 THR B 66 OG1 CG2 REMARK 470 LEU B 67 CG CD1 CD2 REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 2 CG CD OE1 NE2 REMARK 470 LYS C 11 CB CG CD CE NZ REMARK 470 GLU C 24 CB CG CD OE1 OE2 REMARK 470 LYS C 29 CB CG CD CE NZ REMARK 470 LYS C 33 CB CG CD CE NZ REMARK 470 GLU C 34 CG CD OE1 OE2 REMARK 470 ASP C 39 CB CG OD1 OD2 REMARK 470 GLN C 40 CB CG CD OE1 NE2 REMARK 470 ARG C 42 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 48 CG CD CE NZ REMARK 470 GLU C 51 CB CG CD OE1 OE2 REMARK 470 ARG C 54 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 60 CB CG OD1 ND2 REMARK 470 GLN C 62 CG CD OE1 NE2 REMARK 470 LYS C 63 CB CG CD CE NZ REMARK 470 ASP D 195 CG OD1 OD2 REMARK 470 LYS D 230 CD CE NZ REMARK 470 ASP D 279 CB CG OD1 OD2 REMARK 470 GLU D 299 CD OE1 OE2 REMARK 470 LYS E 6 CD CE NZ REMARK 470 GLU E 24 CD OE1 OE2 REMARK 470 ASP E 39 CG OD1 OD2 REMARK 470 LYS E 48 CD CE NZ REMARK 470 GLU E 51 CG CD OE1 OE2 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 ALA A 156 59.46 -92.34 REMARK 500 ASP A 157 46.19 -102.40 REMARK 500 ASN A 158 -5.53 69.43 REMARK 500 PRO A 176 5.18 -69.10 REMARK 500 ASP A 193 74.99 -150.32 REMARK 500 PRO B 19 19.77 -68.84 REMARK 500 SER B 57 -3.70 68.43 REMARK 500 ASN D 158 -2.46 78.59 REMARK 500 ILE D 266 -17.30 -141.26 REMARK 500 ASP D 277 128.35 -171.02 REMARK 500 ALA E 46 29.22 48.00 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 GOL A 1309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1312 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BOP RELATED DB: PDB REMARK 900 STRUCTURE OF OTUD1 OTU DOMAIN REMARK 900 RELATED ID: 4BOQ RELATED DB: PDB REMARK 900 STRUCTURE OF OTUD2 OTU DOMAIN REMARK 900 RELATED ID: 4BOS RELATED DB: PDB REMARK 900 STRUCTURE OF OTUD2 OTU DOMAIN IN COMPLEX WITH UBIQUITIN K11-LINKED REMARK 900 PEPTIDE REMARK 900 RELATED ID: 4BOU RELATED DB: PDB REMARK 900 STRUCTURE OF OTUD3 OTU DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 CATALYTIC CYSTEINE 160 HAD BEEN MUTATED TO ALANINE TO REMARK 999 PERMIT COMPLEX FORMATION WITH DI-UBIQUITIN DBREF 4BOZ A 132 314 UNP Q5VVQ6 OTU1_HUMAN 132 314 DBREF 4BOZ B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4BOZ C 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4BOZ D 132 314 UNP Q5VVQ6 OTU1_HUMAN 132 314 DBREF 4BOZ E 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 4BOZ ALA A 160 UNP Q5VVQ6 CYS 160 ENGINEERED MUTATION SEQADV 4BOZ ALA D 160 UNP Q5VVQ6 CYS 160 ENGINEERED MUTATION SEQRES 1 A 183 ALA PHE THR LYS ARG GLY ALA SER SER TYR VAL ARG GLU SEQRES 2 A 183 THR LEU PRO VAL LEU THR ARG THR VAL VAL PRO ALA ASP SEQRES 3 A 183 ASN SER ALA LEU PHE THR SER VAL TYR TYR VAL VAL GLU SEQRES 4 A 183 GLY GLY VAL LEU ASN PRO ALA CYS ALA PRO GLU MET ARG SEQRES 5 A 183 ARG LEU ILE ALA GLN ILE VAL ALA SER ASP PRO ASP PHE SEQRES 6 A 183 TYR SER GLU ALA ILE LEU GLY LYS THR ASN GLN GLU TYR SEQRES 7 A 183 CYS ASP TRP ILE LYS ARG ASP ASP THR TRP GLY GLY ALA SEQRES 8 A 183 ILE GLU ILE SER ILE LEU SER LYS PHE TYR GLN CYS GLU SEQRES 9 A 183 ILE CYS VAL VAL ASP THR GLN THR VAL ARG ILE ASP ARG SEQRES 10 A 183 PHE GLY GLU ASP ALA GLY TYR THR LYS ARG VAL LEU LEU SEQRES 11 A 183 ILE TYR ASP GLY ILE HIS TYR ASP PRO LEU GLN ARG ASN SEQRES 12 A 183 PHE PRO ASP PRO ASP THR PRO PRO LEU THR ILE PHE SER SEQRES 13 A 183 SER ASN ASP ASP ILE VAL LEU VAL GLN ALA LEU GLU LEU SEQRES 14 A 183 ALA ASP GLU ALA ARG ARG ARG ARG GLN PHE THR ASP VAL SEQRES 15 A 183 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 GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 183 ALA PHE THR LYS ARG GLY ALA SER SER TYR VAL ARG GLU SEQRES 2 D 183 THR LEU PRO VAL LEU THR ARG THR VAL VAL PRO ALA ASP SEQRES 3 D 183 ASN SER ALA LEU PHE THR SER VAL TYR TYR VAL VAL GLU SEQRES 4 D 183 GLY GLY VAL LEU ASN PRO ALA CYS ALA PRO GLU MET ARG SEQRES 5 D 183 ARG LEU ILE ALA GLN ILE VAL ALA SER ASP PRO ASP PHE SEQRES 6 D 183 TYR SER GLU ALA ILE LEU GLY LYS THR ASN GLN GLU TYR SEQRES 7 D 183 CYS ASP TRP ILE LYS ARG ASP ASP THR TRP GLY GLY ALA SEQRES 8 D 183 ILE GLU ILE SER ILE LEU SER LYS PHE TYR GLN CYS GLU SEQRES 9 D 183 ILE CYS VAL VAL ASP THR GLN THR VAL ARG ILE ASP ARG SEQRES 10 D 183 PHE GLY GLU ASP ALA GLY TYR THR LYS ARG VAL LEU LEU SEQRES 11 D 183 ILE TYR ASP GLY ILE HIS TYR ASP PRO LEU GLN ARG ASN SEQRES 12 D 183 PHE PRO ASP PRO ASP THR PRO PRO LEU THR ILE PHE SER SEQRES 13 D 183 SER ASN ASP ASP ILE VAL LEU VAL GLN ALA LEU GLU LEU SEQRES 14 D 183 ALA ASP GLU ALA ARG ARG ARG ARG GLN PHE THR ASP VAL SEQRES 15 D 183 ASN SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET GOL A1309 6 HET GOL D1312 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *11(H2 O) HELIX 1 1 SER A 159 GLU A 170 1 12 HELIX 2 2 CYS A 178 SER A 192 1 15 HELIX 3 3 SER A 198 GLY A 203 1 6 HELIX 4 4 THR A 205 LYS A 214 1 10 HELIX 5 5 GLY A 221 TYR A 232 1 12 HELIX 6 6 ASP A 291 ARG A 308 1 18 HELIX 7 7 THR B 22 GLY B 35 1 14 HELIX 8 8 THR C 22 GLU C 34 1 13 HELIX 9 9 PRO C 37 GLN C 41 5 5 HELIX 10 10 LEU C 56 ASN C 60 5 5 HELIX 11 11 SER D 159 GLU D 170 1 12 HELIX 12 12 ASN D 175 ALA D 177 5 3 HELIX 13 13 CYS D 178 SER D 192 1 15 HELIX 14 14 SER D 198 GLY D 203 1 6 HELIX 15 15 THR D 205 ARG D 215 1 11 HELIX 16 16 GLY D 221 GLN D 233 1 13 HELIX 17 17 GLY D 250 GLY D 254 5 5 HELIX 18 18 ASP D 290 ARG D 307 1 18 HELIX 19 19 THR E 22 GLY E 35 1 14 SHEET 1 AA 4 VAL A 148 ARG A 151 0 SHEET 2 AA 4 TYR A 268 ASN A 274 -1 O GLN A 272 N THR A 150 SHEET 3 AA 4 LYS A 257 TYR A 263 -1 O LEU A 260 N LEU A 271 SHEET 4 AA 4 ILE A 285 SER A 287 -1 O PHE A 286 N ARG A 258 SHEET 1 AB 5 VAL A 148 ARG A 151 0 SHEET 2 AB 5 TYR A 268 ASN A 274 -1 O GLN A 272 N THR A 150 SHEET 3 AB 5 LYS A 257 TYR A 263 -1 O LEU A 260 N LEU A 271 SHEET 4 AB 5 GLU A 235 ASP A 240 1 O GLU A 235 N VAL A 259 SHEET 5 AB 5 ILE A 246 PHE A 249 -1 O ASP A 247 N VAL A 238 SHEET 1 AC 2 ILE A 285 SER A 287 0 SHEET 2 AC 2 LYS A 257 TYR A 263 -1 O ARG A 258 N PHE A 286 SHEET 1 BA 4 THR B 12 GLU B 16 0 SHEET 2 BA 4 GLN B 2 THR B 7 -1 O ILE B 3 N LEU B 15 SHEET 3 BA 4 THR B 66 LEU B 69 1 O LEU B 67 N LYS B 6 SHEET 4 BA 4 LEU B 43 ILE B 44 -1 O ILE B 44 N HIS B 68 SHEET 1 CA 5 THR C 12 GLU C 16 0 SHEET 2 CA 5 GLN C 2 THR C 7 -1 O ILE C 3 N LEU C 15 SHEET 3 CA 5 THR C 66 VAL C 70 1 O LEU C 67 N LYS C 6 SHEET 4 CA 5 ARG C 42 PHE C 45 -1 O ARG C 42 N VAL C 70 SHEET 5 CA 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 DA 4 VAL D 148 ARG D 151 0 SHEET 2 DA 4 TYR D 268 ASN D 274 -1 O GLN D 272 N THR D 150 SHEET 3 DA 4 LYS D 257 TYR D 263 -1 O LEU D 260 N LEU D 271 SHEET 4 DA 4 PHE D 286 SER D 287 -1 O PHE D 286 N ARG D 258 SHEET 1 DB 5 VAL D 148 ARG D 151 0 SHEET 2 DB 5 TYR D 268 ASN D 274 -1 O GLN D 272 N THR D 150 SHEET 3 DB 5 LYS D 257 TYR D 263 -1 O LEU D 260 N LEU D 271 SHEET 4 DB 5 GLU D 235 ASP D 240 1 O GLU D 235 N VAL D 259 SHEET 5 DB 5 ARG D 245 PHE D 249 -1 O ARG D 245 N ASP D 240 SHEET 1 DC 2 PHE D 286 SER D 287 0 SHEET 2 DC 2 LYS D 257 TYR D 263 -1 O ARG D 258 N PHE D 286 SHEET 1 EA 5 THR E 12 GLU E 16 0 SHEET 2 EA 5 GLN E 2 THR E 7 -1 O ILE E 3 N LEU E 15 SHEET 3 EA 5 THR E 66 LEU E 71 1 O LEU E 67 N LYS E 6 SHEET 4 EA 5 GLN E 41 PHE E 45 -1 O ARG E 42 N VAL E 70 SHEET 5 EA 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45 SITE 1 AC1 4 ALA A 187 GLN A 188 CYS A 210 LYS A 214 SITE 1 AC2 3 ARG D 184 GLN D 188 LYS D 214 CRYST1 174.790 44.220 84.950 90.00 91.41 90.00 C 1 2 1 12 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 0.005721 0.000000 0.000141 0.00000 SCALE2 0.000000 0.022614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011775 0.00000