PDB Short entry for 4BOS HEADER HYDROLASE 22-MAY-13 4BOS TITLE STRUCTURE OF OTUD2 OTU DOMAIN IN COMPLEX WITH UBIQUITIN K11-LINKED TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN THIOESTERASE OTU1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OTU DOMAIN, RESIDUES 147-314; COMPND 5 SYNONYM: DUBA-8, HIV-1-INDUCED PROTEASE 7, HIN-7, HSHIN7, OTU DOMAIN COMPND 6 -CONTAINING PROTEIN 2, OTUD2; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: POLYUBIQUITIN-C; COMPND 12 CHAIN: C, E; COMPND 13 FRAGMENT: RESIDUES 1-76; COMPND 14 SYNONYM: OTUD2; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: OTUD2; COMPND 18 CHAIN: F; COMPND 19 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_PLASMID: 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_PLASMID: POPINK; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 27 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 28 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLACI; SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: POPINK 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 3 20-DEC-23 4BOS 1 REMARK REVDAT 2 31-JUL-19 4BOS 1 REMARK LINK ATOM REVDAT 1 24-JUL-13 4BOS 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. 2.35 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1487 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 44.7381 - 5.2239 1.00 2654 141 0.1868 0.2287 REMARK 3 2 5.2239 - 4.1473 1.00 2535 136 0.1454 0.1654 REMARK 3 3 4.1473 - 3.6233 1.00 2548 143 0.1532 0.2151 REMARK 3 4 3.6233 - 3.2921 1.00 2537 123 0.1745 0.2325 REMARK 3 5 3.2921 - 3.0562 1.00 2517 138 0.2004 0.2409 REMARK 3 6 3.0562 - 2.8761 1.00 2530 124 0.2105 0.2745 REMARK 3 7 2.8761 - 2.7321 1.00 2514 125 0.2047 0.2869 REMARK 3 8 2.7321 - 2.6132 1.00 2475 146 0.2163 0.2970 REMARK 3 9 2.6132 - 2.5126 1.00 2533 126 0.2445 0.3042 REMARK 3 10 2.5126 - 2.4259 1.00 2495 143 0.2537 0.3086 REMARK 3 11 2.4259 - 2.3500 1.00 2456 142 0.2776 0.3556 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.15 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 3871 REMARK 3 ANGLE : 1.139 5275 REMARK 3 CHIRALITY : 0.073 616 REMARK 3 PLANARITY : 0.005 694 REMARK 3 DIHEDRAL : 14.315 1426 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE C-TERMINUS OF CHAIN C IS LINKED REMARK 3 THROUGH AN ISOPEPTIDE BOND TO LYS11 OF CHAIN F AND HAS BEEN REMARK 3 REFINED AS SUCH LINKAGE. REMARK 4 REMARK 4 4BOS 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_1290056959. 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 : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 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 : NI FILTER REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29294 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 53.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.89000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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 (%): 60.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3,350, 100 MM SODIUM ACETATE, REMARK 280 200 MM MAGNESIUM NITRATE, PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG B1312 LIES ON A SPECIAL POSITION. 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 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 PHE B 310 REMARK 465 THR B 311 REMARK 465 ASP B 312 REMARK 465 VAL B 313 REMARK 465 ASN B 314 REMARK 465 GLY E 75 REMARK 465 GLY E 76 REMARK 465 PHE F 4 REMARK 465 VAL F 5 REMARK 465 LYS F 6 REMARK 465 THR F 14 REMARK 465 LEU F 15 REMARK 465 GLU F 16 REMARK 465 VAL F 17 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 ASP B 277 CG OD1 OD2 REMARK 470 ASP B 279 CG OD1 OD2 REMARK 470 LYS C 29 CG CD CE NZ REMARK 470 ASP C 32 CG OD1 OD2 REMARK 470 LYS C 48 CG CD CE NZ REMARK 470 GLN C 62 CG CD OE1 NE2 REMARK 470 LYS C 63 CG CD CE NZ REMARK 470 GLU C 64 CG CD OE1 OE2 REMARK 470 LYS E 11 CG CD CE NZ REMARK 470 GLU E 16 CG CD OE1 OE2 REMARK 470 GLU E 18 CG CD OE1 OE2 REMARK 470 ASN E 25 CG OD1 ND2 REMARK 470 VAL E 26 CG1 CG2 REMARK 470 LYS E 27 CG CD CE NZ REMARK 470 LYS E 29 CG CD CE NZ REMARK 470 LYS E 33 CG CD CE NZ REMARK 470 LYS E 48 CG CD CE NZ REMARK 470 GLN E 49 CG CD OE1 NE2 REMARK 470 GLU E 51 CG CD OE1 OE2 REMARK 470 ASP E 52 CG OD1 OD2 REMARK 470 ARG E 54 CG CD NE CZ NH1 NH2 REMARK 470 LEU E 56 CG CD1 CD2 REMARK 470 GLN E 62 CG CD OE1 NE2 REMARK 470 GLU E 64 CG CD OE1 OE2 REMARK 470 LEU E 73 CG CD1 CD2 REMARK 470 ARG E 74 CG CD NE CZ NH1 NH2 REMARK 470 LEU F 8 CG CD1 CD2 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 C GLY C 76 NZ LYS F 11 1.33 REMARK 500 OD2 ASP A 277 O HOH A 2110 2.15 REMARK 500 OD2 ASP A 290 O HOH A 2112 2.16 REMARK 500 O1 NO3 C 1077 O HOH A 2083 2.17 REMARK 500 OE1 GLU A 303 NH1 ARG A 306 2.18 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 O PHE A 231 NH2 ARG B 184 1554 2.15 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 158 -11.30 91.87 REMARK 500 LYS A 204 179.75 177.90 REMARK 500 ASN B 158 -0.41 76.63 REMARK 500 ILE B 266 -52.68 -131.62 REMARK 500 GLU C 64 10.40 59.29 REMARK 500 GLN E 62 -68.08 -135.74 REMARK 500 LEU F 8 -76.60 -112.65 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 NO3 B 1310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 1311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 C 1077 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 C 1078 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 F 1014 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: 4BOU RELATED DB: PDB REMARK 900 STRUCTURE OF OTUD3 OTU DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATION OF CATALYTIC C160A IN CHAINS A AND B TO PERMIT CO- REMARK 999 CRYSTALLISATION WITH UBIQUITIN COMPLEX REMARK 999 ENTRY REFERS TO A SINGLE PROCESSED CHAIN. UBIQUITIN WAS REMARK 999 SUBSEQUENTLY MODIFIED WITH A PEPTIDE (CHAIN F) THROUGH AN REMARK 999 ISOPEPTIDE LINKAGE FROM IT'S C-TERMINAL GLYCINE TO K11 IN REMARK 999 THE PEPTIDE. REMARK 999 CHAIN F IS A SYNTHETIC PEPTIDE THAT CORRESPOND REMARK 999 TO RESIDUES WITHIN UBIQUITIN THAT HAVE BEEN CHEMICALLY REMARK 999 LINKED TO UBIQUITIN CHAINS C AND E C-TERMINUS, THROUGH THE REMARK 999 PEPTIDE LYS11 NH2 GROUP. DBREF 4BOS A 147 314 UNP Q5VVQ6 OTU1_HUMAN 147 314 DBREF 4BOS B 147 314 UNP Q5VVQ6 OTU1_HUMAN 147 314 DBREF 4BOS C 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4BOS E 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4BOS F 4 17 PDB 4BOS 4BOS 4 17 SEQADV 4BOS GLY A 146 UNP Q5VVQ6 EXPRESSION TAG SEQADV 4BOS ALA A 160 UNP Q5VVQ6 CYS 160 ENGINEERED MUTATION SEQADV 4BOS GLY B 146 UNP Q5VVQ6 EXPRESSION TAG SEQADV 4BOS ALA B 160 UNP Q5VVQ6 CYS 160 ENGINEERED MUTATION SEQRES 1 A 169 GLY PRO VAL LEU THR ARG THR VAL VAL PRO ALA ASP ASN SEQRES 2 A 169 SER ALA LEU PHE THR SER VAL TYR TYR VAL VAL GLU GLY SEQRES 3 A 169 GLY VAL LEU ASN PRO ALA CYS ALA PRO GLU MET ARG ARG SEQRES 4 A 169 LEU ILE ALA GLN ILE VAL ALA SER ASP PRO ASP PHE TYR SEQRES 5 A 169 SER GLU ALA ILE LEU GLY LYS THR ASN GLN GLU TYR CYS SEQRES 6 A 169 ASP TRP ILE LYS ARG ASP ASP THR TRP GLY GLY ALA ILE SEQRES 7 A 169 GLU ILE SER ILE LEU SER LYS PHE TYR GLN CYS GLU ILE SEQRES 8 A 169 CYS VAL VAL ASP THR GLN THR VAL ARG ILE ASP ARG PHE SEQRES 9 A 169 GLY GLU ASP ALA GLY TYR THR LYS ARG VAL LEU LEU ILE SEQRES 10 A 169 TYR ASP GLY ILE HIS TYR ASP PRO LEU GLN ARG ASN PHE SEQRES 11 A 169 PRO ASP PRO ASP THR PRO PRO LEU THR ILE PHE SER SER SEQRES 12 A 169 ASN ASP ASP ILE VAL LEU VAL GLN ALA LEU GLU LEU ALA SEQRES 13 A 169 ASP GLU ALA ARG ARG ARG ARG GLN PHE THR ASP VAL ASN SEQRES 1 B 169 GLY PRO VAL LEU THR ARG THR VAL VAL PRO ALA ASP ASN SEQRES 2 B 169 SER ALA LEU PHE THR SER VAL TYR TYR VAL VAL GLU GLY SEQRES 3 B 169 GLY VAL LEU ASN PRO ALA CYS ALA PRO GLU MET ARG ARG SEQRES 4 B 169 LEU ILE ALA GLN ILE VAL ALA SER ASP PRO ASP PHE TYR SEQRES 5 B 169 SER GLU ALA ILE LEU GLY LYS THR ASN GLN GLU TYR CYS SEQRES 6 B 169 ASP TRP ILE LYS ARG ASP ASP THR TRP GLY GLY ALA ILE SEQRES 7 B 169 GLU ILE SER ILE LEU SER LYS PHE TYR GLN CYS GLU ILE SEQRES 8 B 169 CYS VAL VAL ASP THR GLN THR VAL ARG ILE ASP ARG PHE SEQRES 9 B 169 GLY GLU ASP ALA GLY TYR THR LYS ARG VAL LEU LEU ILE SEQRES 10 B 169 TYR ASP GLY ILE HIS TYR ASP PRO LEU GLN ARG ASN PHE SEQRES 11 B 169 PRO ASP PRO ASP THR PRO PRO LEU THR ILE PHE SER SER SEQRES 12 B 169 ASN ASP ASP ILE VAL LEU VAL GLN ALA LEU GLU LEU ALA SEQRES 13 B 169 ASP GLU ALA ARG ARG ARG ARG GLN PHE THR ASP VAL ASN 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 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 SEQRES 1 F 14 PHE VAL LYS THR LEU THR GLY LYS THR ILE THR LEU GLU SEQRES 2 F 14 VAL HET NO3 B1310 4 HET NO3 B1311 4 HET MG B1312 1 HET NO3 C1077 4 HET NO3 C1078 4 HET NO3 F1014 4 HETNAM NO3 NITRATE ION HETNAM MG MAGNESIUM ION FORMUL 6 NO3 5(N O3 1-) FORMUL 8 MG MG 2+ FORMUL 12 HOH *231(H2 O) HELIX 1 1 SER A 159 GLU A 170 1 12 HELIX 2 2 ASN A 175 ALA A 177 5 3 HELIX 3 3 CYS A 178 SER A 192 1 15 HELIX 4 4 SER A 198 GLY A 203 1 6 HELIX 5 5 THR A 205 ARG A 215 1 11 HELIX 6 6 GLY A 221 GLN A 233 1 13 HELIX 7 7 ASP A 291 GLN A 309 1 19 HELIX 8 8 SER B 159 GLU B 170 1 12 HELIX 9 9 ASN B 175 ALA B 177 5 3 HELIX 10 10 CYS B 178 ASP B 193 1 16 HELIX 11 11 SER B 198 GLY B 203 1 6 HELIX 12 12 THR B 205 ARG B 215 1 11 HELIX 13 13 GLY B 221 GLN B 233 1 13 HELIX 14 14 GLY B 250 GLY B 254 5 5 HELIX 15 15 ASP B 290 ARG B 308 1 19 HELIX 16 16 THR C 22 GLY C 35 1 14 HELIX 17 17 PRO C 37 ASP C 39 5 3 HELIX 18 18 THR E 22 GLU E 34 1 13 HELIX 19 19 PRO E 37 ASP E 39 5 3 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 PHE A 286 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 ARG A 245 PHE A 249 -1 O ARG A 245 N ASP A 240 SHEET 1 AC 2 PHE A 286 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 150 ARG B 151 0 SHEET 2 BA 4 TYR B 268 GLN B 272 -1 O GLN B 272 N THR B 150 SHEET 3 BA 4 LYS B 257 TYR B 263 -1 O LEU B 260 N LEU B 271 SHEET 4 BA 4 PHE B 286 SER B 287 -1 O PHE B 286 N ARG B 258 SHEET 1 BB 5 THR B 150 ARG B 151 0 SHEET 2 BB 5 TYR B 268 GLN B 272 -1 O GLN B 272 N THR B 150 SHEET 3 BB 5 LYS B 257 TYR B 263 -1 O LEU B 260 N LEU B 271 SHEET 4 BB 5 GLU B 235 ASP B 240 1 O GLU B 235 N VAL B 259 SHEET 5 BB 5 ARG B 245 PHE B 249 -1 O ARG B 245 N ASP B 240 SHEET 1 BC 2 PHE B 286 SER B 287 0 SHEET 2 BC 2 LYS B 257 TYR B 263 -1 O ARG B 258 N PHE B 286 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 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 CA 5 GLN C 41 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 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 HIS E 68 LEU E 71 1 N LEU E 69 O 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 CISPEP 1 THR F 9 GLY F 10 0 -2.56 SITE 1 AC1 8 TRP A 212 ALA B 156 ASP B 157 ASN B 158 SITE 2 AC1 8 SER B 159 ALA B 160 HIS B 267 HOH B2022 SITE 1 AC2 4 TYR B 263 GLY B 265 HOH B2068 HOH B2079 SITE 1 AC3 1 GLU B 251 SITE 1 AC4 5 HOH A2047 HOH A2082 HOH A2083 LEU C 71 SITE 2 AC4 5 HOH C2019 SITE 1 AC5 8 ALA A 222 THR C 7 LEU C 8 THR C 9 SITE 2 AC5 8 LEU C 69 VAL C 70 LEU C 71 HOH C2003 SITE 1 AC6 6 HIS A 267 ARG A 306 ARG A 307 THR F 9 SITE 2 AC6 6 GLY F 10 LYS F 11 CRYST1 164.480 164.480 44.730 90.00 90.00 120.00 P 6 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 0.006080 0.003510 0.000000 0.00000 SCALE2 0.000000 0.007020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022356 0.00000