HEADER HYDROLASE/SIGNALING PROTEIN/LIGASE 30-JAN-12 4DHZ TITLE THE STRUCTURE OF H/CEOTUB1-UBIQUITIN ALDEHYDE-UBC13~UB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN THIOESTERASE OTUBAIN-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME OTUB1, OTU DOMAIN-CONTAINING COMPND 6 UBIQUITIN ALDEHYDE-BINDING PROTEIN 1, OTUBAIN-1, HOTU1, UBIQUITIN- COMPND 7 SPECIFIC-PROCESSING PROTEASE OTUB1, DEUBIQUITINATING ENZYME OTUBAIN- COMPND 8 LIKE, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE OTUBAIN-LIKE; COMPND 9 EC: 3.4.19.12; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN ALDEHYDE; COMPND 13 CHAIN: B; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: UBIQUITIN; COMPND 17 CHAIN: E; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 N; COMPND 22 CHAIN: F; COMPND 23 SYNONYM: UBC13, BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME, UBIQUITIN COMPND 24 CARRIER PROTEIN N, UBIQUITIN-PROTEIN LIGASE N; COMPND 25 EC: 6.3.2.19; COMPND 26 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: HUMAN, NEMATODE; SOURCE 4 ORGANISM_TAXID: 9606, 6239; SOURCE 5 GENE: OTUB1, OTB1, OTU1, HSPC263, C25D7.8, OTUB-1; 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: UBC; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: UBC; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 GENE: UBE2N, BLU; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITINATION, HYDROLASE-SIGNALING PROTEIN-LIGASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.WIENER,X.ZHANG,T.WANG,C.WOLBERGER REVDAT 6 15-NOV-17 4DHZ 1 REMARK REVDAT 5 26-JUL-17 4DHZ 1 SOURCE REVDAT 4 04-APR-12 4DHZ 1 JRNL REVDAT 3 14-MAR-12 4DHZ 1 JRNL REVDAT 2 29-FEB-12 4DHZ 1 JRNL REVDAT 1 22-FEB-12 4DHZ 0 JRNL AUTH R.WIENER,X.ZHANG,T.WANG,C.WOLBERGER JRNL TITL THE MECHANISM OF OTUB1-MEDIATED INHIBITION OF JRNL TITL 2 UBIQUITINATION. JRNL REF NATURE V. 483 618 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 22367539 JRNL DOI 10.1038/NATURE10911 REMARK 2 REMARK 2 RESOLUTION. 3.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 17369 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) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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) : 3.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1161 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4370 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.80000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.461 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.377 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.913 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4460 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6052 ; 1.156 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 548 ; 5.820 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;38.352 ;24.515 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 774 ;19.084 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.929 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 685 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3366 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2763 ; 0.518 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4464 ; 0.972 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1697 ; 0.927 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1588 ; 1.712 ; 4.500 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4DHZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18369 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 123.371 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG10000, 0.1 M SODIUM CHLORIDE, REMARK 280 100 MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 34.32650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.16325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.48975 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: E 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 MET A -3 REMARK 465 ALA A -2 REMARK 465 ALA A -1 REMARK 465 GLU A 0 REMARK 465 GLU A 1 REMARK 465 PRO A 2 REMARK 465 GLN A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 LYS A 6 REMARK 465 GLN A 7 REMARK 465 GLU A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 ASP A 13 REMARK 465 SER A 14 REMARK 465 GLU A 15 REMARK 465 GLY A 16 REMARK 465 VAL A 17 REMARK 465 ASN A 18 REMARK 465 CYS A 19 REMARK 465 SER A 276 REMARK 465 THR A 277 REMARK 465 GLU A 278 REMARK 465 ALA A 279 REMARK 465 SER A 280 REMARK 465 GLU A 281 REMARK 465 ILE A 282 REMARK 465 GLU A 283 REMARK 465 ASN A 284 REMARK 465 LEU E 573 REMARK 465 ARG E 574 REMARK 465 GLY E 575 REMARK 465 CYS E 576 REMARK 465 MET F 1 REMARK 465 ALA F 2 REMARK 465 ILE F 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 LEU A 20 CG CD1 CD2 REMARK 470 TYR A 22 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 23 CG OD1 OD2 REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 ASP A 31 CG OD1 OD2 REMARK 470 GLN A 34 CG CD OE1 NE2 REMARK 470 GLU A 36 CG CD OE1 OE2 REMARK 470 ILE A 37 CG1 CG2 CD1 REMARK 470 VAL A 39 CG1 CG2 REMARK 470 GLN B 502 CG CD OE1 NE2 REMARK 470 ARG E 572 CG CD NE CZ NH1 NH2 REMARK 470 GLU F 26 CG CD OE1 OE2 REMARK 470 LYS F 92 CG CD CE NZ REMARK 470 ASN F 116 CG OD1 ND2 REMARK 470 GLN F 135 CG CD OE1 NE2 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 ALA A 55 -31.99 -38.38 REMARK 500 GLU A 60 -63.95 -101.38 REMARK 500 SER A 62 63.76 -151.12 REMARK 500 ASP A 129 -89.12 -42.89 REMARK 500 GLU A 194 17.56 54.26 REMARK 500 PRO B 519 -8.91 -55.75 REMARK 500 PRO B 538 -38.73 -39.94 REMARK 500 ARG B 554 -178.06 -69.65 REMARK 500 GLU E 534 89.50 -164.74 REMARK 500 ALA E 546 18.91 52.75 REMARK 500 GLU E 564 72.04 55.60 REMARK 500 VAL E 570 -167.35 -116.92 REMARK 500 PHE F 47 34.32 -93.05 REMARK 500 LYS F 92 -106.11 -120.90 REMARK 500 PRO F 115 98.06 -55.00 REMARK 500 ASP F 119 56.56 -164.06 REMARK 500 PRO F 120 25.88 -71.81 REMARK 500 ASN F 132 106.78 -160.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 575 GLZ B 576 -144.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DHI RELATED DB: PDB REMARK 900 RELATED ID: 4DHJ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING REMARK 999 RESIDUES 1-45 OF UNP Q96FW1 AND RESIDUES 42-284 OF UNP Q9XVR6. DBREF 4DHZ A -3 41 UNP Q96FW1 OTUB1_HUMAN 1 45 DBREF 4DHZ A 42 284 UNP Q9XVR6 OTUBL_CAEEL 42 284 DBREF 4DHZ B 501 576 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4DHZ E 501 576 UNP P0CG48 UBC_HUMAN 1 76 DBREF 4DHZ F 1 152 UNP P61088 UBE2N_HUMAN 1 152 SEQADV 4DHZ CYS E 576 UNP P0CG48 GLY 76 ENGINEERED MUTATION SEQRES 1 A 288 MET ALA ALA GLU GLU PRO GLN GLN GLN LYS GLN GLU PRO SEQRES 2 A 288 LEU GLY SER ASP SER GLU GLY VAL ASN CYS LEU ALA TYR SEQRES 3 A 288 ASP GLU ALA ILE MET ALA GLN GLN ASP ARG ILE GLN GLN SEQRES 4 A 288 GLU ILE ALA VAL GLN ASN PRO LEU VAL ALA THR LEU ALA SEQRES 5 A 288 PRO PHE SER ILE LEU CYS ALA GLU TYR ASP ASN GLU THR SEQRES 6 A 288 SER ALA ALA PHE LEU SER LYS ALA THR GLU LEU SER GLU SEQRES 7 A 288 VAL TYR GLY GLU ILE ARG TYR ILE ARG GLY ASP GLY ASN SEQRES 8 A 288 CYS PHE TYR ARG ALA ILE LEU VAL GLY LEU ILE GLU ILE SEQRES 9 A 288 MET LEU LYS ASP ARG ALA ARG LEU GLU LYS PHE ILE ALA SEQRES 10 A 288 SER SER ARG ASP TRP THR ARG THR LEU VAL GLU LEU GLY SEQRES 11 A 288 PHE PRO ASP TRP THR CYS THR ASP PHE CYS ASP PHE PHE SEQRES 12 A 288 ILE GLU PHE LEU GLU LYS ILE HIS SER GLY VAL HIS THR SEQRES 13 A 288 GLU GLU ALA VAL TYR THR ILE LEU ASN ASP ASP GLY SER SEQRES 14 A 288 ALA ASN TYR ILE LEU MET PHE PHE ARG LEU ILE THR SER SEQRES 15 A 288 ALA PHE LEU LYS GLN ASN SER GLU GLU TYR ALA PRO PHE SEQRES 16 A 288 ILE ASP GLU GLY MET THR VAL ALA GLN TYR CYS GLU GLN SEQRES 17 A 288 GLU ILE GLU PRO MET TRP LYS ASP ALA ASP HIS LEU ALA SEQRES 18 A 288 ILE ASN SER LEU ILE LYS ALA ALA GLY THR ARG VAL ARG SEQRES 19 A 288 ILE GLU TYR MET ASP ARG THR ALA ALA PRO ASN GLY GLY SEQRES 20 A 288 TRP HIS TYR ASP ILE PRO SER ASP ASP GLN GLN ILE ALA SEQRES 21 A 288 PRO GLU ILE THR LEU LEU TYR ARG PRO GLY HIS TYR ASP SEQRES 22 A 288 VAL ILE TYR LYS LYS ASP SER THR GLU ALA SER GLU ILE SEQRES 23 A 288 GLU ASN 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 GLZ SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY CYS SEQRES 1 F 152 MET ALA GLY LEU PRO ARG ARG ILE ILE LYS GLU THR GLN SEQRES 2 F 152 ARG LEU LEU ALA GLU PRO VAL PRO GLY ILE LYS ALA GLU SEQRES 3 F 152 PRO ASP GLU SER ASN ALA ARG TYR PHE HIS VAL VAL ILE SEQRES 4 F 152 ALA GLY PRO GLN ASP SER PRO PHE GLU GLY GLY THR PHE SEQRES 5 F 152 LYS LEU GLU LEU PHE LEU PRO GLU GLU TYR PRO MET ALA SEQRES 6 F 152 ALA PRO LYS VAL ARG PHE MET THR LYS ILE TYR HIS PRO SEQRES 7 F 152 ASN VAL ASP LYS LEU GLY ARG ILE CYS LEU ASP ILE LEU SEQRES 8 F 152 LYS ASP LYS TRP SER PRO ALA LEU GLN ILE ARG THR VAL SEQRES 9 F 152 LEU LEU SER ILE GLN ALA LEU LEU SER ALA PRO ASN PRO SEQRES 10 F 152 ASP ASP PRO LEU ALA ASN ASP VAL ALA GLU GLN TRP LYS SEQRES 11 F 152 THR ASN GLU ALA GLN ALA ILE GLU THR ALA ARG ALA TRP SEQRES 12 F 152 THR ARG LEU TYR ALA MET ASN ASN ILE MODRES 4DHZ GLZ B 576 GLY AMINO-ACETALDEHYDE HET GLZ B 576 4 HETNAM GLZ AMINO-ACETALDEHYDE FORMUL 2 GLZ C2 H5 N O HELIX 1 1 TYR A 22 ALA A 28 1 7 HELIX 2 2 ALA A 28 ASN A 41 1 14 HELIX 3 3 PHE A 50 ALA A 55 1 6 HELIX 4 4 SER A 62 VAL A 75 1 14 HELIX 5 5 ASN A 87 LEU A 102 1 16 HELIX 6 6 ASP A 104 LEU A 125 1 22 HELIX 7 7 PRO A 128 GLY A 149 1 22 HELIX 8 8 THR A 152 LEU A 160 1 9 HELIX 9 9 ASP A 162 ASN A 184 1 23 HELIX 10 10 ASN A 184 ALA A 189 1 6 HELIX 11 11 PRO A 190 ILE A 192 5 3 HELIX 12 12 THR A 197 ILE A 206 1 10 HELIX 13 13 ASP A 214 GLY A 226 1 13 HELIX 14 14 THR B 522 GLU B 534 1 13 HELIX 15 15 PRO B 537 ASP B 539 5 3 HELIX 16 16 THR B 555 ASN B 560 5 6 HELIX 17 17 ILE E 523 GLU E 534 1 12 HELIX 18 18 LEU E 556 ASN E 560 5 5 HELIX 19 19 PRO F 5 GLU F 18 1 14 HELIX 20 20 LEU F 88 LYS F 92 5 5 HELIX 21 21 GLN F 100 ALA F 110 1 11 HELIX 22 22 ASN F 123 ASN F 132 1 10 HELIX 23 23 ASN F 132 ALA F 148 1 17 SHEET 1 A 6 ALA A 48 PRO A 49 0 SHEET 2 A 6 TYR A 76 ARG A 80 -1 O ILE A 79 N ALA A 48 SHEET 3 A 6 HIS A 267 LYS A 273 -1 O VAL A 270 N ARG A 80 SHEET 4 A 6 ILE A 259 ARG A 264 -1 N ARG A 264 O HIS A 267 SHEET 5 A 6 VAL A 229 TYR A 233 1 N GLU A 232 O TYR A 263 SHEET 6 A 6 TRP A 244 ILE A 248 -1 O TYR A 246 N ILE A 231 SHEET 1 B 5 LYS B 511 GLU B 516 0 SHEET 2 B 5 GLN B 502 THR B 507 -1 N VAL B 505 O ILE B 513 SHEET 3 B 5 THR B 566 LEU B 571 1 O LEU B 567 N PHE B 504 SHEET 4 B 5 GLN B 541 PHE B 545 -1 N ILE B 544 O HIS B 568 SHEET 5 B 5 LYS B 548 GLN B 549 -1 O LYS B 548 N PHE B 545 SHEET 1 C 4 THR E 512 GLU E 516 0 SHEET 2 C 4 GLN E 502 LYS E 506 -1 N VAL E 505 O ILE E 513 SHEET 3 C 4 THR E 566 LEU E 571 1 O LEU E 567 N PHE E 504 SHEET 4 C 4 GLN E 541 ILE E 544 -1 N ILE E 544 O HIS E 568 SHEET 1 D 4 ILE F 23 PRO F 27 0 SHEET 2 D 4 TYR F 34 ALA F 40 -1 O VAL F 38 N LYS F 24 SHEET 3 D 4 THR F 51 PHE F 57 -1 O LEU F 54 N VAL F 37 SHEET 4 D 4 LYS F 68 PHE F 71 -1 O LYS F 68 N PHE F 57 LINK C GLY B 575 N GLZ B 576 1555 1555 1.34 LINK SG CYS A 88 C GLZ B 576 1555 1555 1.77 CISPEP 1 ILE A 248 PRO A 249 0 5.42 CISPEP 2 TYR F 62 PRO F 63 0 6.73 CISPEP 3 SER F 113 ALA F 114 0 22.08 CISPEP 4 PRO F 117 ASP F 118 0 1.62 CISPEP 5 ASP F 118 ASP F 119 0 -13.40 CISPEP 6 MET F 149 ASN F 150 0 -8.63 CRYST1 123.371 123.371 68.653 90.00 90.00 90.00 P 41 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 0.008106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014566 0.00000