PDB Short entry for 5L8H HEADER HYDROLASE 07-JUN-16 5L8H TITLE STRUCTURE OF USP46-UBVME COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 46; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 46,UBIQUITIN THIOESTERASE 46, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 46; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: POLYUBIQUITIN-B; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: RECOMBINANT EXPRESSION FOLLOWED BY CHEMICAL SYNTHESIS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP46; 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 UBIQUITIN SPECIFIC PROTEASE, DEUBIQUITINATING ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.CLERICI,T.SIXMA,S.DHARADHAR REVDAT 5 10-JAN-24 5L8H 1 REMARK REVDAT 4 15-NOV-23 5L8H 1 LINK ATOM REVDAT 3 07-DEC-16 5L8H 1 REVDAT 2 30-NOV-16 5L8H 1 JRNL REVDAT 1 28-SEP-16 5L8H 0 JRNL AUTH S.DHARADHAR,M.CLERICI,W.J.VAN DIJK,A.FISH,T.K.SIXMA JRNL TITL A CONSERVED TWO-STEP BINDING FOR THE UAF1 REGULATOR TO THE JRNL TITL 2 USP12 DEUBIQUITINATING ENZYME. JRNL REF J.STRUCT.BIOL. V. 196 437 2016 JRNL REFN ESSN 1095-8657 JRNL PMID 27650958 JRNL DOI 10.1016/J.JSB.2016.09.011 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 52516 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2764 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3857 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 202 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31000 REMARK 3 B22 (A**2) : 0.66000 REMARK 3 B33 (A**2) : -0.35000 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): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.073 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3247 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3130 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4376 ; 1.758 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7204 ; 1.031 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 5.997 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;35.559 ;24.451 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 616 ;14.139 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.078 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 489 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3636 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 766 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1549 ; 1.718 ; 2.107 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1546 ; 1.716 ; 2.107 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1932 ; 2.795 ; 3.134 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1930 ; 2.792 ; 3.134 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1696 ; 2.158 ; 2.457 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1697 ; 2.158 ; 2.456 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2444 ; 3.580 ; 3.552 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3719 ; 6.746 ;26.207 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3624 ; 6.620 ;25.373 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 31 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5000 52.8070 15.6640 REMARK 3 T TENSOR REMARK 3 T11: 0.0958 T22: 0.0122 REMARK 3 T33: 0.0940 T12: -0.0053 REMARK 3 T13: 0.0401 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 0.8270 L22: 1.6048 REMARK 3 L33: 1.5700 L12: 0.7759 REMARK 3 L13: 0.9089 L23: 0.5854 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: 0.0404 S13: -0.1003 REMARK 3 S21: -0.1132 S22: 0.0683 S23: -0.2731 REMARK 3 S31: -0.1317 S32: 0.0337 S33: -0.0873 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 164 A 248 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9780 32.4160 34.0320 REMARK 3 T TENSOR REMARK 3 T11: 0.0924 T22: 0.0229 REMARK 3 T33: 0.0710 T12: 0.0041 REMARK 3 T13: -0.0113 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.2440 L22: 2.2747 REMARK 3 L33: 0.5933 L12: 0.3399 REMARK 3 L13: -0.2140 L23: -1.1509 REMARK 3 S TENSOR REMARK 3 S11: -0.0125 S12: -0.0234 S13: -0.0760 REMARK 3 S21: 0.2946 S22: 0.0128 S23: 0.0246 REMARK 3 S31: -0.1333 S32: 0.0036 S33: -0.0003 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 249 A 361 REMARK 3 ORIGIN FOR THE GROUP (A): 6.9310 48.2780 18.7470 REMARK 3 T TENSOR REMARK 3 T11: 0.0875 T22: 0.0506 REMARK 3 T33: 0.0598 T12: 0.0054 REMARK 3 T13: -0.0272 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.9532 L22: 0.5937 REMARK 3 L33: 1.5584 L12: 0.5932 REMARK 3 L13: -0.6456 L23: -0.1311 REMARK 3 S TENSOR REMARK 3 S11: 0.1245 S12: 0.0393 S13: 0.0128 REMARK 3 S21: -0.0349 S22: -0.0240 S23: 0.0558 REMARK 3 S31: -0.1310 S32: -0.2374 S33: -0.1005 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 75 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0150 26.6720 21.4720 REMARK 3 T TENSOR REMARK 3 T11: 0.0704 T22: 0.0059 REMARK 3 T33: 0.1099 T12: 0.0169 REMARK 3 T13: 0.0254 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.6169 L22: 2.5735 REMARK 3 L33: 1.0487 L12: 0.1488 REMARK 3 L13: -0.0658 L23: -1.5631 REMARK 3 S TENSOR REMARK 3 S11: -0.0825 S12: -0.0365 S13: -0.1939 REMARK 3 S21: -0.2540 S22: -0.0370 S23: -0.1803 REMARK 3 S31: 0.0906 S32: 0.0061 S33: 0.1196 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 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 REMARK 4 REMARK 4 5L8H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55291 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 28.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.560 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: 2IBI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.96M SODIUM CITRATE PH7.5 AND 0.1MM REMARK 280 ZINC CHLORIDE CRYO - 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.65500 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 1.000000 0.000000 0.000000 45.97500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.97500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.65500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.97500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.33000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.65500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.97500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.33000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 A1261 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1271 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 8 REMARK 465 ILE A 9 REMARK 465 CYS A 10 REMARK 465 ASN A 11 REMARK 465 MET A 12 REMARK 465 GLY A 13 REMARK 465 THR A 14 REMARK 465 ASN A 15 REMARK 465 ALA A 16 REMARK 465 SER A 17 REMARK 465 ALA A 18 REMARK 465 LEU A 19 REMARK 465 GLU A 20 REMARK 465 LYS A 21 REMARK 465 ASP A 22 REMARK 465 ILE A 23 REMARK 465 GLY A 24 REMARK 465 PRO A 25 REMARK 465 GLU A 26 REMARK 465 GLN A 27 REMARK 465 PHE A 28 REMARK 465 PRO A 29 REMARK 465 ILE A 30 REMARK 465 GLU A 143 REMARK 465 LYS A 144 REMARK 465 GLN A 145 REMARK 465 ASN A 146 REMARK 465 GLY A 147 REMARK 465 LYS A 148 REMARK 465 LEU A 149 REMARK 465 LYS A 150 REMARK 465 ASN A 151 REMARK 465 GLY A 152 REMARK 465 ASN A 153 REMARK 465 MET A 154 REMARK 465 ASN A 155 REMARK 465 GLU A 156 REMARK 465 PRO A 157 REMARK 465 ALA A 158 REMARK 465 GLU A 159 REMARK 465 ASN A 160 REMARK 465 ASN A 161 REMARK 465 LYS A 162 REMARK 465 PRO A 163 REMARK 465 SER A 287 REMARK 465 ASP A 288 REMARK 465 ALA A 289 REMARK 465 VAL A 290 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 ARG A 60 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU A 112 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -5.5 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 ASN A 115 -178.96 -170.49 REMARK 500 SER A 223 -119.61 56.44 REMARK 500 ASP A 329 -112.48 43.85 REMARK 500 TYR A 358 -40.39 -130.88 REMARK 500 LEU B 71 -148.10 -110.13 REMARK 500 REMARK 500 REMARK: NULL 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 A1000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 182 SG REMARK 620 2 CYS A 185 SG 106.3 REMARK 620 3 CYS A 229 SG 108.6 102.5 REMARK 620 4 CYS A 232 SG 113.2 109.9 115.5 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 ZN A 1000 DBREF 5L8H A 8 366 UNP P62068 UBP46_HUMAN 8 366 DBREF 5L8H B 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 5L8H VAL A 46 UNP P62068 CYS 46 CONFLICT SEQADV 5L8H ARG A 265 UNP P62068 HIS 265 CONFLICT SEQADV 5L8H GVE B 76 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQRES 1 A 359 SER ILE CYS ASN MET GLY THR ASN ALA SER ALA LEU GLU SEQRES 2 A 359 LYS ASP ILE GLY PRO GLU GLN PHE PRO ILE ASN GLU HIS SEQRES 3 A 359 TYR PHE GLY LEU VAL ASN PHE GLY ASN THR CYS TYR VAL SEQRES 4 A 359 ASN SER VAL LEU GLN ALA LEU TYR PHE CYS ARG PRO PHE SEQRES 5 A 359 ARG GLU ASN VAL LEU ALA TYR LYS ALA GLN GLN LYS LYS SEQRES 6 A 359 LYS GLU ASN LEU LEU THR CYS LEU ALA ASP LEU PHE HIS SEQRES 7 A 359 SER ILE ALA THR GLN LYS LYS LYS VAL GLY VAL ILE PRO SEQRES 8 A 359 PRO LYS LYS PHE ILE SER ARG LEU ARG LYS GLU ASN ASP SEQRES 9 A 359 LEU PHE ASP ASN TYR MET GLN GLN ASP ALA HIS GLU PHE SEQRES 10 A 359 LEU ASN TYR LEU LEU ASN THR ILE ALA ASP ILE LEU GLN SEQRES 11 A 359 GLU GLU LYS LYS GLN GLU LYS GLN ASN GLY LYS LEU LYS SEQRES 12 A 359 ASN GLY ASN MET ASN GLU PRO ALA GLU ASN ASN LYS PRO SEQRES 13 A 359 GLU LEU THR TRP VAL HIS GLU ILE PHE GLN GLY THR LEU SEQRES 14 A 359 THR ASN GLU THR ARG CYS LEU ASN CYS GLU THR VAL SER SEQRES 15 A 359 SER LYS ASP GLU ASP PHE LEU ASP LEU SER VAL ASP VAL SEQRES 16 A 359 GLU GLN ASN THR SER ILE THR HIS CYS LEU ARG ASP PHE SEQRES 17 A 359 SER ASN THR GLU THR LEU CYS SER GLU GLN LYS TYR TYR SEQRES 18 A 359 CYS GLU THR CYS CYS SER LYS GLN GLU ALA GLN LYS ARG SEQRES 19 A 359 MET ARG VAL LYS LYS LEU PRO MET ILE LEU ALA LEU HIS SEQRES 20 A 359 LEU LYS ARG PHE LYS TYR MET GLU GLN LEU ARG ARG TYR SEQRES 21 A 359 THR LYS LEU SER TYR ARG VAL VAL PHE PRO LEU GLU LEU SEQRES 22 A 359 ARG LEU PHE ASN THR SER SER ASP ALA VAL ASN LEU ASP SEQRES 23 A 359 ARG MET TYR ASP LEU VAL ALA VAL VAL VAL HIS CYS GLY SEQRES 24 A 359 SER GLY PRO ASN ARG GLY HIS TYR ILE THR ILE VAL LYS SEQRES 25 A 359 SER HIS GLY PHE TRP LEU LEU PHE ASP ASP ASP ILE VAL SEQRES 26 A 359 GLU LYS ILE ASP ALA GLN ALA ILE GLU GLU PHE TYR GLY SEQRES 27 A 359 LEU THR SER ASP ILE SER LYS ASN SER GLU SER GLY TYR SEQRES 28 A 359 ILE LEU PHE TYR GLN SER ARG GLU 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 GVE HET GVE B 76 8 HET ZN A1000 1 HETNAM GVE METHYL 4-AMINOBUTANOATE HETNAM ZN ZINC ION FORMUL 2 GVE C5 H11 N O2 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *250(H2 O) HELIX 1 AA1 THR A 43 PHE A 55 1 13 HELIX 2 AA2 CYS A 56 GLN A 70 1 15 HELIX 3 AA3 ASN A 75 GLN A 90 1 16 HELIX 4 AA4 PRO A 99 ASN A 110 1 12 HELIX 5 AA5 ASP A 111 ASP A 114 5 4 HELIX 6 AA6 ALA A 121 LYS A 141 1 21 HELIX 7 AA7 THR A 166 GLN A 173 1 8 HELIX 8 AA8 ILE A 208 SER A 216 1 9 HELIX 9 AA9 CYS A 222 LYS A 226 5 5 HELIX 10 AB1 ASP A 336 GLY A 345 5 10 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 TYR A 34 LEU A 37 0 SHEET 2 AA1 2 VAL A 94 ILE A 97 1 O ILE A 97 N GLY A 36 SHEET 1 AA2 2 GLN A 119 ASP A 120 0 SHEET 2 AA2 2 ARG B 74 GLY B 75 -1 O GLY B 75 N GLN A 119 SHEET 1 AA3 4 VAL A 188 PHE A 195 0 SHEET 2 AA3 4 GLY A 174 CYS A 182 -1 N ASN A 178 O LYS A 191 SHEET 3 AA3 4 ALA A 238 LYS A 246 -1 O GLN A 239 N ARG A 181 SHEET 4 AA3 4 GLU A 219 LEU A 221 -1 N LEU A 221 O ALA A 238 SHEET 1 AA4 5 LEU A 198 VAL A 200 0 SHEET 2 AA4 5 ILE A 250 LEU A 255 1 O HIS A 254 N LEU A 198 SHEET 3 AA4 5 SER A 354 SER A 364 -1 O LEU A 360 N LEU A 253 SHEET 4 AA4 5 ASP A 293 GLY A 306 -1 N VAL A 302 O ILE A 359 SHEET 5 AA4 5 GLU A 279 PHE A 283 -1 N LEU A 282 O ARG A 294 SHEET 1 AA5 7 LEU A 198 VAL A 200 0 SHEET 2 AA5 7 ILE A 250 LEU A 255 1 O HIS A 254 N LEU A 198 SHEET 3 AA5 7 SER A 354 SER A 364 -1 O LEU A 360 N LEU A 253 SHEET 4 AA5 7 ASP A 293 GLY A 306 -1 N VAL A 302 O ILE A 359 SHEET 5 AA5 7 HIS A 313 SER A 320 -1 O ILE A 315 N VAL A 303 SHEET 6 AA5 7 PHE A 323 ASP A 328 -1 O PHE A 327 N THR A 316 SHEET 7 AA5 7 ILE A 331 ILE A 335 -1 O GLU A 333 N LEU A 326 SHEET 1 AA6 2 THR A 206 SER A 207 0 SHEET 2 AA6 2 VAL A 274 VAL A 275 1 O VAL A 275 N THR A 206 SHEET 1 AA7 2 TYR A 227 CYS A 229 0 SHEET 2 AA7 2 SER A 234 GLN A 236 -1 O GLN A 236 N TYR A 227 SHEET 1 AA8 2 PHE A 258 MET A 261 0 SHEET 2 AA8 2 ARG A 266 LYS A 269 -1 O ARG A 266 N MET A 261 SHEET 1 AA9 5 THR B 12 GLU B 16 0 SHEET 2 AA9 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA9 5 THR B 66 VAL B 70 1 O LEU B 67 N LYS B 6 SHEET 4 AA9 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA9 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SSBOND 1 CYS A 222 CYS A 222 1555 3555 1.97 LINK SG CYS A 44 CB GVE B 76 1555 1555 1.80 LINK C GLY B 75 N GVE B 76 1555 1555 1.34 LINK SG CYS A 182 ZN ZN A1000 1555 1555 2.37 LINK SG CYS A 185 ZN ZN A1000 1555 1555 2.24 LINK SG CYS A 229 ZN ZN A1000 1555 1555 2.30 LINK SG CYS A 232 ZN ZN A1000 1555 1555 2.36 SITE 1 AC1 4 CYS A 182 CYS A 185 CYS A 229 CYS A 232 CRYST1 91.950 104.660 135.310 90.00 90.00 90.00 C 2 2 21 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 0.010875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007390 0.00000