HEADER HYDROLASE 18-FEB-13 3ZNX TITLE CRYSTAL STRUCTURE OF THE OTU DOMAIN OF OTULIN D336A MUTANT 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 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 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 3ZNX 1 REMARK LINK REVDAT 1 26-JUN-13 3ZNX 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. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 63440 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) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3382 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4635 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 250 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2094 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.03000 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): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.416 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2400 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2336 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3304 ; 1.462 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5423 ; 1.000 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 5.628 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;32.837 ;24.397 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 450 ;12.849 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;21.292 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 369 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2762 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 555 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 896 ; 0.347 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2155 ; 0.222 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1136 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1280 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 70 ; 0.311 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 6 ; 0.353 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.097 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 84 ; 0.354 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 48 ; 0.228 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.059 ; 0.200 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): 1125 ; 3.222 ; 1.553 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1124 ; 3.206 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1423 ; 3.734 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1275 ; 5.721 ; 1.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1845 ; 6.607 ; 1.500 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): 2387 ;10.739 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2308 ;20.514 ; 5.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. RESIDUES 187,206,217,252,325,338 HAVE DISORDERED SIDE REMARK 3 CHAINS AND WERE DELETED UNTIL VISIBLE ELECTRON DENSITY. REMARK 3 DISORDERED SIDE CHAINS WERE PRUNED ACCORDING TO INTERPRETATION REMARK 3 OF THE ELECTRON DENSITY REMARK 4 REMARK 4 3ZNX 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_1290055869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 47.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3ZNV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES/IMIDAZOLE PH 6.5, 30 MM REMARK 280 MGCL2, 30 MM CACL2, 10% PEG 4,000, 20% GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.90350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.42150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.09850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.42150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.90350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.09850 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 VAL A 346 REMARK 465 CYS A 347 REMARK 465 GLU A 348 REMARK 465 GLU A 349 REMARK 465 THR A 350 REMARK 465 SER A 351 REMARK 465 LEU A 352 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 187 CD CE NZ REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 217 CD OE1 OE2 REMARK 470 GLU A 252 CG CD OE1 OE2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 ARG A 338 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 239 O HOH A 2226 1.18 REMARK 500 OE1 GLN A 137 O HOH A 2099 1.60 REMARK 500 OD2 ASP A 90 O HOH A 2020 1.72 REMARK 500 SG CYS A 105 O HOH A 2043 1.86 REMARK 500 OD1 ASP A 90 O HOH A 2019 1.88 REMARK 500 O HOH A 2163 O HOH A 2224 1.91 REMARK 500 OE2 GLU A 224 O HOH A 2223 1.94 REMARK 500 OG SER A 163 O HOH A 2146 1.95 REMARK 500 O HOH A 2085 O HOH A 2086 1.97 REMARK 500 OD1 ASP A 90 O HOH A 2021 2.02 REMARK 500 O HOH A 2264 O HOH A 2267 2.05 REMARK 500 O HOH A 2099 O HOH A 2100 2.05 REMARK 500 OE1 GLU A 287 O HOH A 2255 2.07 REMARK 500 NZ LYS A 107 O HOH A 2027 2.09 REMARK 500 O HOH A 2229 O HOH A 2231 2.12 REMARK 500 OE2 GLU A 204 O HOH A 2204 2.13 REMARK 500 O HOH A 2327 O HOH A 2328 2.18 REMARK 500 NE2 GLN A 115 O HOH A 2055 2.19 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 OE2 GLU A 112 O HOH A 2065 4465 1.99 REMARK 500 O HOH A 2026 O HOH A 2285 4565 2.06 REMARK 500 O HOH A 2007 O HOH A 2146 2674 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 209 CD GLU A 209 OE1 0.111 REMARK 500 CYS A 215 CB CYS A 215 SG -0.105 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 337 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 219 63.91 -100.00 REMARK 500 SER A 266 37.78 -144.09 REMARK 500 HIS A 276 -62.56 -128.20 REMARK 500 HIS A 282 -62.20 -120.68 REMARK 500 ASN A 311 33.06 -89.19 REMARK 500 ALA A 336 33.65 -144.44 REMARK 500 ALA A 336 -153.70 -129.08 REMARK 500 ASP A 337 26.92 49.39 REMARK 500 ARG A 338 -58.95 -121.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2106 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A2330 DISTANCE = 7.32 ANGSTROMS 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 CA A1346 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 163 O REMARK 620 2 GLU A 209 OE2 107.9 REMARK 620 3 GLN A 212 OE1 127.2 81.9 REMARK 620 4 HOH A2208 O 77.0 79.8 153.6 REMARK 620 5 HOH A2212 O 86.4 163.9 95.5 96.8 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 CA A 1346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1349 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1350 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. DBREF 3ZNX A 80 352 UNP Q96BN8 F105B_HUMAN 80 352 SEQADV 3ZNX GLY A 78 UNP Q96BN8 EXPRESSION TAG SEQADV 3ZNX PRO A 79 UNP Q96BN8 EXPRESSION TAG SEQADV 3ZNX ALA A 336 UNP Q96BN8 ASP 336 ENGINEERED MUTATION 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 CYS 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 ALA ASP SEQRES 21 A 275 ARG HIS TYR ASN ILE PRO VAL ARG VAL CYS GLU GLU THR SEQRES 22 A 275 SER LEU HET CA A1346 1 HET CL A1347 1 HET GOL A1348 6 HET GOL A1349 6 HET GOL A1350 6 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA CA 2+ FORMUL 3 CL CL 1- FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *330(H2 O) HELIX 1 1 ILE A 88 TRP A 96 1 9 HELIX 2 2 THR A 100 GLN A 115 1 16 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 TYR A 165 1 14 HELIX 6 6 ASN A 166 TRP A 171 5 6 HELIX 7 7 ASP A 183 MET A 205 1 23 HELIX 8 8 THR A 207 PHE A 219 1 13 HELIX 9 9 GLU A 222 LYS A 249 1 28 HELIX 10 10 PRO A 254 ARG A 263 1 10 HELIX 11 11 ASP A 268 HIS A 276 1 9 HELIX 12 12 LEU A 277 VAL A 280 5 4 HELIX 13 13 GLU A 287 ARG A 299 1 13 HELIX 14 14 SER A 308 TYR A 310 5 3 HELIX 15 15 THR A 312 GLU A 314 5 3 SHEET 1 AA 6 MET A 86 ASP A 87 0 SHEET 2 AA 6 SER A 119 ARG A 121 -1 O ILE A 120 N MET A 86 SHEET 3 AA 6 TYR A 340 VAL A 344 -1 O ILE A 342 N ARG A 121 SHEET 4 AA 6 VAL A 329 ALA A 334 -1 O ILE A 333 N ASN A 341 SHEET 5 AA 6 THR A 301 ARG A 306 1 O THR A 301 N VAL A 330 SHEET 6 AA 6 ILE A 316 TYR A 319 -1 O THR A 317 N VAL A 304 LINK O SER A 163 CA CA A1346 2674 1555 2.48 LINK OE2 GLU A 209 CA CA A1346 1555 1555 2.93 LINK OE1BGLN A 212 CA CA A1346 1555 1555 2.47 LINK CA CA A1346 O HOH A2208 1555 1555 2.28 LINK CA CA A1346 O HOH A2212 1555 1555 2.41 CISPEP 1 TYR A 319 PRO A 320 0 -12.22 SITE 1 AC1 4 SER A 163 GLU A 209 HOH A2208 HOH A2212 SITE 1 AC2 2 LYS A 94 VAL A 318 SITE 1 AC3 8 TRP A 167 ASP A 268 PRO A 269 GLY A 270 SITE 2 AC3 8 GLN A 271 ARG A 274 HOH A2161 HOH A2327 SITE 1 AC4 7 LEU A 235 ASN A 238 ARG A 239 GLU A 242 SITE 2 AC4 7 HOH A2123 HOH A2230 HOH A2329 SITE 1 AC5 7 HIS A 276 GLN A 279 VAL A 280 GLY A 285 SITE 2 AC5 7 GLU A 287 GLU A 290 HOH A2269 CRYST1 43.807 72.197 94.843 90.00 90.00 90.00 P 21 21 21 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 0.022827 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010544 0.00000