HEADER HYDROLASE 18-FEB-13 3ZNZ TITLE CRYSTAL STRUCTURE OF OTULIN OTU DOMAIN (C129A) IN COMPLEX WITH MET1- TITLE 2 DI UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FAM105B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: OTU DOMAIN, RESIDUES 80-352; COMPND 5 EC: 3.4.19.12; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: POLYUBIQUITIN-C; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: MET1-DI UBIQUITIN; COMPND 12 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: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA PLACI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: POPINF; 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: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21; 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 K.KEUSEKOTTEN,P.R.ELLIOTT,L.GLOCKNER,Y.KULATHU,T.WAUER,D.KRAPPMANN, AUTHOR 2 K.HOFMANN,D.KOMANDER REVDAT 2 20-DEC-23 3ZNZ 1 REMARK REVDAT 1 26-JUN-13 3ZNZ 0 JRNL AUTH K.KEUSEKOTTEN,P.R.ELLIOTT,L.GLOCKNER,B.K.FIIL,R.B.DAMGAARD, JRNL AUTH 2 Y.KULATHU,T.WAUER,M.K.HOSPENTHAL,M.GYRD-HANSEN,D.KRAPPMANN, JRNL AUTH 3 K.HOFMANN,D.KOMANDER JRNL TITL OTULIN ANTAGONIZES LUBAC SIGNALING BY SPECIFICALLY JRNL TITL 2 HYDROLYZING MET1-LINKED POLYUBIQUITIN. JRNL REF CELL(CAMBRIDGE,MASS.) V. 153 1312 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23746843 JRNL DOI 10.1016/J.CELL.2013.05.014 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42965 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2168 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 42.8127 - 4.6839 1.00 2919 126 0.1862 0.1780 REMARK 3 2 4.6839 - 3.7184 1.00 2757 149 0.1458 0.1821 REMARK 3 3 3.7184 - 3.2486 1.00 2749 149 0.1666 0.1979 REMARK 3 4 3.2486 - 2.9516 1.00 2735 141 0.1918 0.2094 REMARK 3 5 2.9516 - 2.7401 1.00 2698 167 0.1952 0.2463 REMARK 3 6 2.7401 - 2.5786 1.00 2722 145 0.1935 0.2499 REMARK 3 7 2.5786 - 2.4495 1.00 2684 151 0.1899 0.2274 REMARK 3 8 2.4495 - 2.3429 1.00 2697 140 0.1904 0.2849 REMARK 3 9 2.3429 - 2.2527 1.00 2720 134 0.1900 0.2379 REMARK 3 10 2.2527 - 2.1749 1.00 2672 141 0.1948 0.2609 REMARK 3 11 2.1749 - 2.1069 1.00 2728 123 0.1928 0.2727 REMARK 3 12 2.1069 - 2.0467 1.00 2694 150 0.2074 0.2716 REMARK 3 13 2.0467 - 1.9928 1.00 2661 148 0.2135 0.2877 REMARK 3 14 1.9928 - 1.9442 1.00 2687 157 0.2337 0.2887 REMARK 3 15 1.9442 - 1.9000 1.00 2674 147 0.2587 0.3316 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 49.95 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.40910 REMARK 3 B22 (A**2) : 4.40910 REMARK 3 B33 (A**2) : -8.81810 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 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 : 0.007 3447 REMARK 3 ANGLE : 1.018 4680 REMARK 3 CHIRALITY : 0.070 524 REMARK 3 PLANARITY : 0.004 599 REMARK 3 DIHEDRAL : 14.864 1319 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: RESIDUES 93,94,153,160,187,197,222 FROM REMARK 3 CHAIN A AND RESIDUES 48,63 FROM CHAIN B HAVE DISORDERED SIDE REMARK 3 CHAINS AND WERE TRIMMED TO THE CORRESPONDING ELECTRON DENSITY. REMARK 4 REMARK 4 3ZNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1290055880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.9795 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 : 42974 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 3ZNV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, 2M (NH4)2SO4, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 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 SMTRY1 7 1.000000 0.000000 0.000000 50.01000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.87329 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 93.42000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 50.01000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 28.87329 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 93.42000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 50.01000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 28.87329 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 93.42000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 50.01000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 28.87329 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 93.42000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 50.01000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 28.87329 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 93.42000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 50.01000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 28.87329 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 93.42000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.74657 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 186.84000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 57.74657 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 186.84000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 57.74657 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 186.84000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 57.74657 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 186.84000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 57.74657 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 186.84000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 57.74657 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 186.84000 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: 4890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 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 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 HOH A2031 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2057 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2191 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 LEU A 175 REMARK 465 LYS A 176 REMARK 465 PHE A 177 REMARK 465 ASP A 178 REMARK 465 GLY A 179 REMARK 465 LYS A 180 REMARK 465 ASN A 181 REMARK 465 GLU A 182 REMARK 465 LEU A 352 REMARK 465 LEU B 147 REMARK 465 ARG B 148 REMARK 465 LEU B 149 REMARK 465 ARG B 150 REMARK 465 GLY B 151 REMARK 465 GLY B 152 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 LYS A 93 CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 LYS A 160 CE NZ REMARK 470 LYS A 187 CE NZ REMARK 470 LYS A 197 CD CE NZ REMARK 470 GLU A 222 CG CD OE1 OE2 REMARK 470 LYS B 48 CD CE NZ REMARK 470 LYS B 63 CD CE NZ 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 2133 O HOH A 2240 2.00 REMARK 500 O HOH A 2133 O HOH B 2007 2.13 REMARK 500 O2 SO4 A 1356 O HOH A 2215 2.14 REMARK 500 O HOH A 2143 O HOH A 2262 2.16 REMARK 500 O3 SO4 A 1355 O HOH A 2266 2.17 REMARK 500 O HOH A 2274 O HOH A 2277 2.18 REMARK 500 O HOH A 2275 O HOH B 2024 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 O3 SO4 A 1354 O HOH A 2155 2555 2.07 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 127 -3.79 72.66 REMARK 500 SER A 266 39.88 -143.02 REMARK 500 HIS A 276 -55.18 -130.30 REMARK 500 HIS A 282 -84.75 -127.11 REMARK 500 ASP A 336 52.69 -149.17 REMARK 500 ASP A 337 16.31 57.86 REMARK 500 LEU B 8 34.51 -72.82 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 SO4 A 1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1356 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1148 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZNV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN AT 1.3 ANGSTROMS. REMARK 900 RELATED ID: 3ZNX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN D336A MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAIN B: THE LAST THREE RESIDUES (RGG) ARE PART OF THE SECOND REMARK 999 UBIQUITIN SEQUENCE. THE UNIPROT ENTRY REFERS TO A GENE REMARK 999 PRODUCT OF UB WHICH IS CLEAVED WITHIN CELLS TO YIELD REMARK 999 MONO UB (FIRST HALF OF THE SEQUENCE). THE AUTHORS ENGINEERED REMARK 999 A DI-UB MOLECULE FROM THE FUSION OF TWO UB ORFS. REMARK 999 MET1-DI UBIQUITIN IS FORMED FROM THE FUSION OF A SECOND REMARK 999 UBIQUITIN TO THE 3' CDNA OF UBIQUITIN. REMARK 999 CHAIN A: CYS129 MUTATED TO ALA TO PERMIT CO-CRYSTALLISATION WITH REMARK 999 MET1-DIUB. DBREF 3ZNZ A 80 352 UNP Q96BN8 F105B_HUMAN 80 352 DBREF 3ZNZ B 1 149 UNP F5H265 F5H265_HUMAN 1 149 SEQADV 3ZNZ GLY A 78 UNP Q96BN8 EXPRESSION TAG SEQADV 3ZNZ PRO A 79 UNP Q96BN8 EXPRESSION TAG SEQADV 3ZNZ ALA A 129 UNP Q96BN8 CYS 129 ENGINEERED MUTATION SEQADV 3ZNZ ARG B 150 UNP F5H265 SEE REMARK 999 SEQADV 3ZNZ GLY B 151 UNP F5H265 SEE REMARK 999 SEQADV 3ZNZ GLY B 152 UNP F5H265 SEE REMARK 999 SEQRES 1 A 275 GLY PRO LEU SER VAL ALA PRO GLU MET ASP ILE MET ASP SEQRES 2 A 275 TYR CYS LYS LYS GLU TRP ARG GLY ASN THR GLN LYS ALA SEQRES 3 A 275 THR CYS MET LYS MET GLY TYR GLU GLU VAL SER GLN LYS SEQRES 4 A 275 PHE THR SER ILE ARG ARG VAL ARG GLY ASP ASN TYR ALA SEQRES 5 A 275 ALA LEU ARG ALA THR LEU PHE GLN ALA MET SER GLN ALA SEQRES 6 A 275 VAL GLY LEU PRO PRO TRP LEU GLN ASP PRO GLU LEU MET SEQRES 7 A 275 LEU LEU PRO GLU LYS LEU ILE SER LYS TYR ASN TRP ILE SEQRES 8 A 275 LYS GLN TRP LYS LEU GLY LEU LYS PHE ASP GLY LYS ASN SEQRES 9 A 275 GLU ASP LEU VAL ASP LYS ILE LYS GLU SER LEU THR LEU SEQRES 10 A 275 LEU ARG LYS LYS TRP ALA GLY LEU ALA GLU MET ARG THR SEQRES 11 A 275 ALA GLU ALA ARG GLN ILE ALA CYS ASP GLU LEU PHE THR SEQRES 12 A 275 ASN GLU ALA GLU GLU TYR SER LEU TYR GLU ALA VAL LYS SEQRES 13 A 275 PHE LEU MET LEU ASN ARG ALA ILE GLU LEU TYR ASN ASP SEQRES 14 A 275 LYS GLU LYS GLY LYS GLU VAL PRO PHE PHE SER VAL LEU SEQRES 15 A 275 LEU PHE ALA ARG ASP THR SER ASN ASP PRO GLY GLN LEU SEQRES 16 A 275 LEU ARG ASN HIS LEU ASN GLN VAL GLY HIS THR GLY GLY SEQRES 17 A 275 LEU GLU GLN VAL GLU MET PHE LEU LEU ALA TYR ALA VAL SEQRES 18 A 275 ARG HIS THR ILE GLN VAL TYR ARG LEU SER LYS TYR ASN SEQRES 19 A 275 THR GLU GLU PHE ILE THR VAL TYR PRO THR ASP PRO PRO SEQRES 20 A 275 LYS ASP TRP PRO VAL VAL THR LEU ILE ALA GLU ASP ASP SEQRES 21 A 275 ARG HIS TYR ASN ILE PRO VAL ARG VAL CYS GLU GLU THR SEQRES 22 A 275 SER LEU SEQRES 1 B 152 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 152 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 152 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 152 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 152 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 152 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MET GLN SEQRES 7 B 152 ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE THR LEU SEQRES 8 B 152 GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS ALA SEQRES 9 B 152 LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN SEQRES 10 B 152 ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP GLY ARG SEQRES 11 B 152 THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER THR LEU SEQRES 12 B 152 HIS LEU VAL LEU ARG LEU ARG GLY GLY HET SO4 A1352 5 HET SO4 A1353 5 HET SO4 A1354 5 HET SO4 A1355 5 HET SO4 A1356 5 HET SO4 B1147 5 HET SO4 B1148 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 7(O4 S 2-) FORMUL 10 HOH *370(H2 O) HELIX 1 1 ILE A 88 TRP A 96 1 9 HELIX 2 2 THR A 100 SER A 114 1 15 HELIX 3 3 TYR A 128 GLN A 141 1 14 HELIX 4 4 PRO A 146 ASP A 151 1 6 HELIX 5 5 PRO A 152 MET A 155 5 4 HELIX 6 6 LEU A 156 TYR A 165 1 10 HELIX 7 7 ASN A 166 TRP A 171 5 6 HELIX 8 8 ASP A 183 GLU A 204 1 22 HELIX 9 9 THR A 207 PHE A 219 1 13 HELIX 10 10 ASN A 221 LYS A 249 1 29 HELIX 11 11 PRO A 254 PHE A 261 1 8 HELIX 12 12 ASP A 268 HIS A 276 1 9 HELIX 13 13 GLN A 288 ARG A 299 1 12 HELIX 14 14 SER A 308 TYR A 310 5 3 HELIX 15 15 ARG A 345 GLU A 349 5 5 HELIX 16 16 THR B 22 GLY B 35 1 14 HELIX 17 17 PRO B 37 GLN B 41 5 5 HELIX 18 18 LEU B 56 ASN B 60 5 5 HELIX 19 19 THR B 98 GLY B 111 1 14 HELIX 20 20 PRO B 113 GLN B 117 5 5 HELIX 21 21 LEU B 132 ASN B 136 5 5 SHEET 1 AA 3 MET A 86 ASP A 87 0 SHEET 2 AA 3 SER A 119 ARG A 121 -1 O ILE A 120 N MET A 86 SHEET 3 AA 3 ILE A 342 VAL A 344 -1 O ILE A 342 N ARG A 121 SHEET 1 AB 2 LEU A 286 GLU A 287 0 SHEET 2 AB 2 ARG B 74 GLY B 75 -1 O GLY B 75 N LEU A 286 SHEET 1 AC 3 ILE A 316 TYR A 319 0 SHEET 2 AC 3 THR A 301 ARG A 306 -1 O ILE A 302 N TYR A 319 SHEET 3 AC 3 VAL A 329 ALA A 334 1 O VAL A 330 N GLN A 303 SHEET 1 BA 5 THR B 12 GLU B 16 0 SHEET 2 BA 5 GLN B 2 LYS B 6 -1 O ILE B 3 N LEU B 15 SHEET 3 BA 5 THR B 66 LEU B 69 1 O LEU B 67 N LYS B 6 SHEET 4 BA 5 LEU B 43 PHE B 45 -1 O ILE B 44 N HIS B 68 SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 BB 5 THR B 88 GLU B 92 0 SHEET 2 BB 5 GLN B 78 LYS B 82 -1 O ILE B 79 N LEU B 91 SHEET 3 BB 5 THR B 142 VAL B 146 1 O LEU B 143 N LYS B 82 SHEET 4 BB 5 ARG B 118 PHE B 121 -1 O ARG B 118 N VAL B 146 SHEET 5 BB 5 LYS B 124 GLN B 125 -1 O LYS B 124 N PHE B 121 CISPEP 1 TYR A 319 PRO A 320 0 -2.00 SITE 1 AC1 4 GLN A 271 ARG A 274 ASN A 275 HOH A2209 SITE 1 AC2 5 ARG A 299 HOH A2101 HOH A2179 HOH A2255 SITE 2 AC2 5 HOH A2271 SITE 1 AC3 6 ARG A 97 THR A 207 HOH A2154 HOH A2155 SITE 2 AC3 6 HOH A2272 THR B 85 SITE 1 AC4 6 ARG A 338 HOH A2038 HOH A2266 HOH A2274 SITE 2 AC4 6 HOH A2276 GLY B 35 SITE 1 AC5 5 GLY A 281 HIS A 282 HOH A2215 HOH A2278 SITE 2 AC5 5 LYS B 139 SITE 1 AC6 6 ASP A 264 THR A 265 HOH A2201 ARG B 42 SITE 2 AC6 6 GLN B 49 ARG B 72 SITE 1 AC7 3 ARG B 74 SER B 133 HOH B2079 CRYST1 100.020 100.020 280.260 90.00 90.00 120.00 H 3 2 18 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 0.009998 0.005772 0.000000 0.00000 SCALE2 0.000000 0.011545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003568 0.00000