HEADER HYDROLASE 17-NOV-16 5TXK TITLE CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 35,UBIQUITIN COMPND 3 CARBOXYL-TERMINAL HYDROLASE 35; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 432-603,UNP RESIDUES 754-944; COMPND 6 SYNONYM: DEUBIQUITINATING ENZYME 35,UBIQUITIN THIOESTERASE 35, COMPND 7 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 35,DEUBIQUITINATING ENZYME 35, COMPND 8 UBIQUITIN THIOESTERASE 35,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 35; COMPND 9 EC: 3.4.19.12,3.4.19.12; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: POLYUBIQUITIN-B; COMPND 13 CHAIN: B; 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 GENE: USP35, KIAA1372, USP34; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEUBIQUITINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.BADER,A.WEISS-PUXBAUM,A.ZOEPHEL REVDAT 3 16-OCT-19 5TXK 1 REMARK REVDAT 2 30-MAY-18 5TXK 1 JRNL REVDAT 1 09-MAY-18 5TXK 0 JRNL AUTH P.LEZNICKI,J.NATARAJAN,G.BADER,W.SPEVAK,A.SCHLATTL, JRNL AUTH 2 S.A.ABDUL REHMAN,D.PATHAK,S.WEIDLICH,A.ZOEPHEL,M.C.BORDONE, JRNL AUTH 3 N.L.BARBOSA-MORAIS,G.BOEHMELT,Y.KULATHU JRNL TITL EXPANSION OF DUB FUNCTIONALITY GENERATED BY ALTERNATIVE JRNL TITL 2 ISOFORMS - USP35, A CASE STUDY. JRNL REF J. CELL. SCI. V. 131 2018 JRNL REFN ESSN 1477-9137 JRNL PMID 29685892 JRNL DOI 10.1242/JCS.212753 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.11.6 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 51309 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1983 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.89 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3741 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2089 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3599 REMARK 3 BIN R VALUE (WORKING SET) : 0.2081 REMARK 3 BIN FREE R VALUE : 0.2286 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3131 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 683 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.70620 REMARK 3 B22 (A**2) : -0.70620 REMARK 3 B33 (A**2) : 1.41250 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.174 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.110 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.100 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.097 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.093 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3263 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4410 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1150 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 76 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 470 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3263 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 418 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4311 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.63 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.89 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|434 - A|520 } REMARK 3 ORIGIN FOR THE GROUP (A): 78.7303 79.7270 39.4504 REMARK 3 T TENSOR REMARK 3 T11: -0.0210 T22: -0.0276 REMARK 3 T33: -0.0357 T12: -0.0345 REMARK 3 T13: -0.0192 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.8532 L22: 0.9156 REMARK 3 L33: 0.9332 L12: 0.0342 REMARK 3 L13: -0.1194 L23: -0.1245 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: -0.0210 S13: 0.0458 REMARK 3 S21: 0.0888 S22: -0.0402 S23: -0.1049 REMARK 3 S31: -0.1311 S32: 0.1696 S33: 0.0334 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|521 - A|550 } REMARK 3 ORIGIN FOR THE GROUP (A): 65.0538 79.2240 52.3057 REMARK 3 T TENSOR REMARK 3 T11: 0.0099 T22: -0.0191 REMARK 3 T33: -0.0285 T12: 0.0052 REMARK 3 T13: 0.0098 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.7708 L22: 1.6751 REMARK 3 L33: 5.7572 L12: -0.9235 REMARK 3 L13: -0.3631 L23: 2.1292 REMARK 3 S TENSOR REMARK 3 S11: -0.1720 S12: -0.1778 S13: 0.0156 REMARK 3 S21: 0.2396 S22: 0.1050 S23: 0.0386 REMARK 3 S31: -0.0266 S32: -0.1201 S33: 0.0670 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|551 - A|593 } REMARK 3 ORIGIN FOR THE GROUP (A): 47.6255 81.4905 42.5923 REMARK 3 T TENSOR REMARK 3 T11: -0.0120 T22: -0.0040 REMARK 3 T33: -0.0112 T12: -0.0088 REMARK 3 T13: -0.0026 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.8301 L22: 0.0938 REMARK 3 L33: 0.0385 L12: -0.0298 REMARK 3 L13: -0.0083 L23: 0.0708 REMARK 3 S TENSOR REMARK 3 S11: -0.0501 S12: -0.1583 S13: 0.0863 REMARK 3 S21: -0.0054 S22: -0.0124 S23: 0.0380 REMARK 3 S31: -0.0817 S32: -0.0781 S33: 0.0626 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { A|594 - A|927 } REMARK 3 ORIGIN FOR THE GROUP (A): 59.1525 78.1250 26.7782 REMARK 3 T TENSOR REMARK 3 T11: -0.0008 T22: -0.0076 REMARK 3 T33: -0.0369 T12: -0.0237 REMARK 3 T13: -0.0152 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.9511 L22: 0.3483 REMARK 3 L33: 0.3660 L12: 0.1735 REMARK 3 L13: -0.3882 L23: -0.0935 REMARK 3 S TENSOR REMARK 3 S11: -0.0580 S12: 0.1606 S13: 0.0615 REMARK 3 S21: -0.0513 S22: 0.0265 S23: 0.0250 REMARK 3 S31: -0.0040 S32: -0.0790 S33: 0.0315 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { B|1 - B|22 } REMARK 3 ORIGIN FOR THE GROUP (A): 45.8422 64.7290 39.2932 REMARK 3 T TENSOR REMARK 3 T11: -0.0137 T22: -0.0124 REMARK 3 T33: -0.0096 T12: -0.0002 REMARK 3 T13: 0.0379 T23: -0.0325 REMARK 3 L TENSOR REMARK 3 L11: 2.5010 L22: 0.2156 REMARK 3 L33: 1.0366 L12: 0.5350 REMARK 3 L13: -0.1195 L23: -0.0605 REMARK 3 S TENSOR REMARK 3 S11: -0.0915 S12: -0.0340 S13: -0.1122 REMARK 3 S21: 0.0717 S22: 0.0134 S23: 0.0247 REMARK 3 S31: 0.2352 S32: -0.1403 S33: 0.0781 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { B|23 - B|44 } REMARK 3 ORIGIN FOR THE GROUP (A): 54.1147 59.1284 37.1316 REMARK 3 T TENSOR REMARK 3 T11: -0.0279 T22: -0.0187 REMARK 3 T33: 0.0175 T12: -0.0263 REMARK 3 T13: 0.0140 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 1.5911 L22: 3.9619 REMARK 3 L33: 0.8944 L12: 0.1120 REMARK 3 L13: -0.5306 L23: -0.7162 REMARK 3 S TENSOR REMARK 3 S11: -0.0321 S12: -0.0498 S13: -0.1551 REMARK 3 S21: 0.0831 S22: 0.0835 S23: 0.0480 REMARK 3 S31: 0.1527 S32: -0.0185 S33: -0.0514 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: { B|45 - B|56 } REMARK 3 ORIGIN FOR THE GROUP (A): 57.0719 67.1334 46.2282 REMARK 3 T TENSOR REMARK 3 T11: 0.0176 T22: -0.0046 REMARK 3 T33: -0.0250 T12: 0.0004 REMARK 3 T13: 0.0080 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 3.6730 L22: 0.0269 REMARK 3 L33: 3.5965 L12: 0.0514 REMARK 3 L13: -0.8720 L23: 0.4135 REMARK 3 S TENSOR REMARK 3 S11: 0.0583 S12: -0.2869 S13: 0.0901 REMARK 3 S21: 0.1848 S22: -0.0293 S23: -0.1162 REMARK 3 S31: 0.0667 S32: 0.0851 S33: -0.0290 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: { B|57 - B|76 } REMARK 3 ORIGIN FOR THE GROUP (A): 54.7386 68.1034 40.3222 REMARK 3 T TENSOR REMARK 3 T11: 0.0083 T22: -0.0073 REMARK 3 T33: -0.0038 T12: 0.0047 REMARK 3 T13: 0.0023 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.7872 L22: 0.5165 REMARK 3 L33: 1.4067 L12: -0.0243 REMARK 3 L13: -0.8495 L23: -0.1241 REMARK 3 S TENSOR REMARK 3 S11: -0.0876 S12: -0.1182 S13: -0.0219 REMARK 3 S21: 0.1226 S22: -0.0077 S23: 0.0301 REMARK 3 S31: -0.0925 S32: -0.0803 S33: 0.0953 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000223832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51309 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 47.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.95 M AMMONIUM SULPHATE 0.1 M HEPES, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 53.19050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.11750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.11750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.78575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.11750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.11750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.59525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.11750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.11750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.78575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.11750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.11750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.59525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.19050 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: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 A1406 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1632 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 SER A 423 REMARK 465 GLU A 424 REMARK 465 LEU A 425 REMARK 465 ALA A 426 REMARK 465 GLY A 427 REMARK 465 PHE A 428 REMARK 465 TYR A 429 REMARK 465 PRO A 430 REMARK 465 ARG A 431 REMARK 465 LEU A 432 REMARK 465 MET A 433 REMARK 465 PRO A 552 REMARK 465 SER A 553 REMARK 465 PRO A 554 REMARK 465 PRO A 555 REMARK 465 GLU A 556 REMARK 465 GLU A 557 REMARK 465 PRO A 558 REMARK 465 PRO A 559 REMARK 465 ALA A 560 REMARK 465 PRO A 561 REMARK 465 GLY A 754 REMARK 465 SER A 755 REMARK 465 GLU A 756 REMARK 465 GLY A 757 REMARK 465 PRO A 874 REMARK 465 ALA A 875 REMARK 465 ALA A 876 REMARK 465 SER A 877 REMARK 465 LEU A 878 REMARK 465 GLY A 879 REMARK 465 THR A 880 REMARK 465 ALA A 881 REMARK 465 ASP A 882 REMARK 465 ARG A 883 REMARK 465 PRO A 884 REMARK 465 GLU A 885 REMARK 465 PRO A 886 REMARK 465 ARG A 928 REMARK 465 GLU A 929 REMARK 465 GLY A 930 REMARK 465 PRO A 931 REMARK 465 GLU A 932 REMARK 465 ALA A 933 REMARK 465 GLU A 934 REMARK 465 LEU A 935 REMARK 465 GLY A 936 REMARK 465 SER A 937 REMARK 465 SER A 938 REMARK 465 ARG A 939 REMARK 465 VAL A 940 REMARK 465 ARG A 941 REMARK 465 THR A 942 REMARK 465 GLU A 943 REMARK 465 PRO A 944 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 548 CG CD OE1 NE2 REMARK 480 GLU A 887 CB CG CD OE1 OE2 REMARK 480 ASN A 888 N CG OD1 ND2 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 OE1 GLU A 887 O HOH A 1101 1.66 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 GLN A 478 79.69 -117.86 REMARK 500 ALA A 776 -116.42 47.36 REMARK 500 ASP A 895 -118.29 51.74 REMARK 500 SER A 901 -154.94 -144.47 REMARK 500 VAL A 909 -71.70 -32.88 REMARK 500 LEU B 71 -148.68 -109.90 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 A1638 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1639 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1640 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A1641 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A1642 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1643 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A1644 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A1645 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A1646 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A1647 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A1648 DISTANCE = 10.55 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 ZN A1006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 580 SG REMARK 620 2 CYS A 583 SG 108.1 REMARK 620 3 CYS A 782 SG 107.8 105.4 REMARK 620 4 CYS A 785 SG 111.7 108.9 114.5 REMARK 620 N 1 2 3 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 DBREF 5TXK A 423 603 UNP Q9P2H5 UBP35_HUMAN 423 603 DBREF 5TXK A 754 944 UNP Q9P2H5 UBP35_HUMAN 754 944 DBREF 5TXK B 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 SEQADV 5TXK SER A 450 UNP Q9P2H5 CYS 450 ENGINEERED MUTATION SEQRES 1 A 372 SER GLU LEU ALA GLY PHE TYR PRO ARG LEU MET ALA LYS SEQRES 2 A 372 SER ASP THR GLY LYS ILE GLY LEU ILE ASN LEU GLY ASN SEQRES 3 A 372 THR SER TYR VAL ASN SER ILE LEU GLN ALA LEU PHE MET SEQRES 4 A 372 ALA SER ASP PHE ARG HIS CYS VAL LEU ARG LEU THR GLU SEQRES 5 A 372 ASN ASN SER GLN PRO LEU MET THR LYS LEU GLN TRP LEU SEQRES 6 A 372 PHE GLY PHE LEU GLU HIS SER GLN ARG PRO ALA ILE SER SEQRES 7 A 372 PRO GLU ASN PHE LEU SER ALA SER TRP THR PRO TRP PHE SEQRES 8 A 372 SER PRO GLY THR GLN GLN ASP CYS SER GLU TYR LEU LYS SEQRES 9 A 372 TYR LEU LEU ASP ARG LEU HIS GLU GLU GLU LYS THR GLY SEQRES 10 A 372 THR ARG ILE CYS GLN LYS LEU LYS GLN SER SER SER PRO SEQRES 11 A 372 SER PRO PRO GLU GLU PRO PRO ALA PRO SER SER THR SER SEQRES 12 A 372 VAL GLU LYS MET PHE GLY GLY LYS ILE VAL THR ARG ILE SEQRES 13 A 372 CYS CYS LEU CYS CYS LEU ASN VAL SER SER ARG GLU GLU SEQRES 14 A 372 ALA PHE THR ASP LEU SER LEU ALA PHE PRO PRO PRO GLY SEQRES 15 A 372 SER GLU GLY SER ARG SER VAL LEU ASP LEU VAL ASN TYR SEQRES 16 A 372 PHE LEU SER PRO GLU LYS LEU THR ALA GLU ASN ARG TYR SEQRES 17 A 372 TYR CYS GLU SER CYS ALA SER LEU GLN ASP ALA GLU LYS SEQRES 18 A 372 VAL VAL GLU LEU SER GLN GLY PRO CYS TYR LEU ILE LEU SEQRES 19 A 372 THR LEU LEU ARG PHE SER PHE ASP LEU ARG THR MET ARG SEQRES 20 A 372 ARG ARG LYS ILE LEU ASP ASP VAL SER ILE PRO LEU LEU SEQRES 21 A 372 LEU ARG LEU PRO LEU ALA GLY GLY ARG GLY GLN ALA TYR SEQRES 22 A 372 ASP LEU CYS SER VAL VAL VAL HIS SER GLY VAL SER SER SEQRES 23 A 372 GLU SER GLY HIS TYR TYR CYS TYR ALA ARG GLU GLY ALA SEQRES 24 A 372 ALA ARG PRO ALA ALA SER LEU GLY THR ALA ASP ARG PRO SEQRES 25 A 372 GLU PRO GLU ASN GLN TRP TYR LEU PHE ASN ASP THR ARG SEQRES 26 A 372 VAL SER PHE SER SER PHE GLU SER VAL SER ASN VAL THR SEQRES 27 A 372 SER PHE PHE PRO LYS ASP THR ALA TYR VAL LEU PHE TYR SEQRES 28 A 372 ARG GLN ARG PRO ARG GLU GLY PRO GLU ALA GLU LEU GLY SEQRES 29 A 372 SER SER ARG VAL ARG THR GLU PRO 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 HET SO4 A1001 5 HET SO4 A1002 5 HET SO4 A1003 5 HET EDO A1004 4 HET EDO A1005 4 HET ZN A1006 1 HET EDO B 101 4 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 EDO 3(C2 H6 O2) FORMUL 8 ZN ZN 2+ FORMUL 10 HOH *683(H2 O) HELIX 1 AA1 THR A 449 ALA A 462 1 14 HELIX 2 AA2 ALA A 462 ARG A 471 1 10 HELIX 3 AA3 GLN A 478 SER A 494 1 17 HELIX 4 AA4 PRO A 501 SER A 508 1 8 HELIX 5 AA5 ASP A 520 SER A 550 1 31 HELIX 6 AA6 THR A 564 GLY A 571 1 8 HELIX 7 AA7 SER A 760 LEU A 769 1 10 HELIX 8 AA8 THR A 775 ARG A 779 5 5 HELIX 9 AA9 ALA A 838 GLY A 840 5 3 HELIX 10 AB1 SER A 902 PHE A 913 1 12 HELIX 11 AB2 THR B 22 GLY B 35 1 14 HELIX 12 AB3 PRO B 37 GLN B 41 5 5 HELIX 13 AB4 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 2 GLY A 442 LEU A 443 0 SHEET 2 AA1 2 ALA A 498 ILE A 499 1 O ILE A 499 N GLY A 442 SHEET 1 AA2 4 VAL A 586 PHE A 593 0 SHEET 2 AA2 4 GLY A 572 CYS A 580 -1 N ILE A 574 O GLU A 591 SHEET 3 AA2 4 ALA A 791 GLN A 799 -1 O GLU A 792 N CYS A 579 SHEET 4 AA2 4 GLU A 772 LEU A 774 -1 N GLU A 772 O LYS A 793 SHEET 1 AA3 5 LEU A 596 LEU A 598 0 SHEET 2 AA3 5 TYR A 803 LEU A 808 1 O THR A 807 N LEU A 596 SHEET 3 AA3 5 ASP A 916 GLN A 925 -1 O TYR A 919 N LEU A 808 SHEET 4 AA3 5 GLY A 842 SER A 854 -1 N VAL A 851 O VAL A 920 SHEET 5 AA3 5 LEU A 832 PRO A 836 -1 N LEU A 835 O GLN A 843 SHEET 1 AA4 7 LEU A 596 LEU A 598 0 SHEET 2 AA4 7 TYR A 803 LEU A 808 1 O THR A 807 N LEU A 596 SHEET 3 AA4 7 ASP A 916 GLN A 925 -1 O TYR A 919 N LEU A 808 SHEET 4 AA4 7 GLY A 842 SER A 854 -1 N VAL A 851 O VAL A 920 SHEET 5 AA4 7 HIS A 862 ALA A 867 -1 O HIS A 862 N SER A 854 SHEET 6 AA4 7 TYR A 891 ASN A 894 -1 O PHE A 893 N CYS A 865 SHEET 7 AA4 7 ARG A 897 PHE A 900 -1 O SER A 899 N LEU A 892 SHEET 1 AA5 2 TYR A 780 CYS A 782 0 SHEET 2 AA5 2 SER A 787 GLN A 789 -1 O GLN A 789 N TYR A 780 SHEET 1 AA6 2 PHE A 811 ASP A 814 0 SHEET 2 AA6 2 ARG A 819 LYS A 822 -1 O ARG A 819 N ASP A 814 SHEET 1 AA7 5 THR B 12 GLU B 16 0 SHEET 2 AA7 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA7 5 THR B 66 VAL B 70 1 O LEU B 67 N LYS B 6 SHEET 4 AA7 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA7 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK SG CYS A 580 ZN ZN A1006 1555 1555 2.35 LINK SG CYS A 583 ZN ZN A1006 1555 1555 2.32 LINK SG CYS A 782 ZN ZN A1006 1555 1555 2.34 LINK SG CYS A 785 ZN ZN A1006 1555 1555 2.35 SITE 1 AC1 8 ARG A 577 SER A 588 SER A 902 PHE A 903 SITE 2 AC1 8 GLU A 904 HOH A1184 HOH A1234 HOH A1348 SITE 1 AC2 5 ARG A 820 HOH A1227 HOH A1319 GLN B 40 SITE 2 AC2 5 ARG B 74 SITE 1 AC3 6 PHE A 490 SER A 494 GLN A 495 ARG A 496 SITE 2 AC3 6 HOH A1217 HOH A1295 SITE 1 AC4 4 TYR A 864 HOH A1157 HOH A1212 HOH A1298 SITE 1 AC5 7 GLU A 567 GLY A 571 THR A 594 HOH A1138 SITE 2 AC5 7 HOH A1144 HOH A1363 HOH B 269 SITE 1 AC6 4 CYS A 580 CYS A 583 CYS A 782 CYS A 785 SITE 1 AC7 6 TRP A 512 GLN A 519 ARG B 72 ARG B 74 SITE 2 AC7 6 HOH B 226 HOH B 267 CRYST1 104.235 104.235 106.381 90.00 90.00 90.00 P 43 21 2 8 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 0.009594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009400 0.00000