HEADER LIGASE 21-OCT-05 2C4O OBSLTE 13-AUG-14 2C4O 2CLW TITLE CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME TITLE 2 UBCH5B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE D2, UBIQUITIN CARRIER COMPND 5 PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, COMPND 6 UBCH5B; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RESIDUE A 85 HAS BEEN MODIFIED FROM COMPND 10 CYSTEINE BY 2-MERCAPTOETHANOL TO FORM S, COMPND 11 S-(2-HYDROXYETHYL)THIOCYSTEINE; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 14 CHAIN: B, C, D; COMPND 15 SYNONYM: UBIQUITIN-PROTEIN LIGASE D2, UBIQUITIN CARRIER COMPND 16 PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, COMPND 17 UBCH5B; COMPND 18 EC: 6.3.2.19; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET VECTOR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM-12 (EMBL); SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 19 EXPRESSION_SYSTEM_VECTOR: PET VECTOR; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PETM-12 (EMBL) KEYWDS THIOESTERIFICATION, UBIQUITIN-CONJUGATING ENZYME, LIGASE, KEYWDS 2 UBL CONJUGATION PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR R.B.DODD,R.J.READ REVDAT 3 13-AUG-14 2C4O 1 OBSLTE REVDAT 2 24-FEB-09 2C4O 1 VERSN REVDAT 1 22-NOV-06 2C4O 0 JRNL AUTH R.B.DODD,R.J.READ JRNL TITL STRUCTURES OF TWO HUMAN UBIQUITIN-CONJUGATING JRNL TITL 2 ENZYMES FROM TWINNED CRYSTALS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : TWIN_LSQ REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1400828.11 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.6 REMARK 3 NUMBER OF REFLECTIONS : 37733 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 SET) : 0.227 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.5 REMARK 3 FREE R VALUE TEST SET COUNT : 1538 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.2 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3926 REMARK 3 BIN R VALUE (WORKING SET) : 0.308 REMARK 3 BIN FREE R VALUE : 0.333 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.8 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 228 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.9 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.91 REMARK 3 B22 (A**2) : -1.72 REMARK 3 B33 (A**2) : 3.63 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.01 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.44 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.48 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.26 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.15 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.58 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.33 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.368832 REMARK 3 BSOL : 46.8589 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : GOL.PAR REMARK 3 PARAMETER FILE 5 : CME.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_CME.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : GOL.TOP REMARK 3 TOPOLOGY FILE 5 : CME.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DUE TO THE PRESENCE OF ORTHORHOMBIC REMARK 3 PSEUDOSYMMETRY, THE TEST SET OF REFLECTIONS WERE CHOSEN IN REMARK 3 P212121 AND THEN EXPANDED TO COVER THE MONOCLINIC SPACE GROUP. REMARK 3 DATA WERE FOUND TO BE NEAR- -PERFECTLY TWINNED AND WERE REMARK 3 THEREFORE TREATED AS PERFECTLY TWINNED. NCS RESTRAINTS WERE REMARK 3 APPLIED DURING REFINEMENT WITH POSITIONAL RESTRAINTS OF 30 REMARK 3 KCAL/MOL-A**2 (300 INITIALLY) AND B-FACTOR TARGET SIGMA OF 2. REMARK 4 REMARK 4 2C4O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-05. REMARK 100 THE PDBE ID CODE IS EBI-26027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9821 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 602165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 30.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1QCQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.1 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM AMMONIUM SULPHATE, 100 REMARK 280 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME REMARK 280 2000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 32.90150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 GENERATING THE BIOMOLECULE 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: PQS 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 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 400 REMARK 400 COMPOUND REMARK 400 CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER REMARK 400 PROTEINS. MEDIATES THE SELECTIVE DEGRADATION OF SHORT-LIVED REMARK 400 AND ABNORMAL PROTEINS. FUNCTIONS IN THE E6/E6-AP-INDUCED REMARK 400 UBIQUITINATION OF P53/TP53. 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 -17 REMARK 465 LYS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 PRO A -9 REMARK 465 MET A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 MET B -17 REMARK 465 LYS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 PRO B -9 REMARK 465 MET B -8 REMARK 465 SER B -7 REMARK 465 GLY B -6 REMARK 465 LEU B -5 REMARK 465 VAL B -4 REMARK 465 PRO B -3 REMARK 465 MET C -17 REMARK 465 LYS C -16 REMARK 465 HIS C -15 REMARK 465 HIS C -14 REMARK 465 HIS C -13 REMARK 465 HIS C -12 REMARK 465 HIS C -11 REMARK 465 HIS C -10 REMARK 465 PRO C -9 REMARK 465 MET C -8 REMARK 465 SER C -7 REMARK 465 GLY C -6 REMARK 465 LEU C -5 REMARK 465 VAL C -4 REMARK 465 PRO C -3 REMARK 465 MET D -17 REMARK 465 LYS D -16 REMARK 465 HIS D -15 REMARK 465 HIS D -14 REMARK 465 HIS D -13 REMARK 465 HIS D -12 REMARK 465 HIS D -11 REMARK 465 HIS D -10 REMARK 465 PRO D -9 REMARK 465 MET D -8 REMARK 465 SER D -7 REMARK 465 GLY D -6 REMARK 465 LEU D -5 REMARK 465 VAL D -4 REMARK 465 PRO D -3 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 GLY A -1 N - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 PRO C 18 N - CA - C ANGL. DEV. = -17.6 DEGREES REMARK 500 PRO C 18 N - CA - CB ANGL. DEV. = -17.6 DEGREES REMARK 500 PRO C 18 N - CD - CG ANGL. DEV. = -17.6 DEGREES REMARK 500 ALA C 19 N - CA - C ANGL. DEV. = 18.7 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 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 PRO A 17 101.24 -46.17 REMARK 500 ALA A 19 126.34 -34.40 REMARK 500 GLN A 20 54.72 -7.88 REMARK 500 PRO A 40 151.42 -47.89 REMARK 500 THR A 58 4.67 -60.22 REMARK 500 ASN A 79 -163.82 -78.48 REMARK 500 ARG A 90 -97.62 -150.59 REMARK 500 HIS B 7 0.89 -69.12 REMARK 500 PRO B 17 102.90 -49.45 REMARK 500 GLN B 20 9.31 44.70 REMARK 500 PRO B 40 153.73 -45.32 REMARK 500 THR B 58 22.99 -67.30 REMARK 500 ASP B 59 13.95 -141.21 REMARK 500 ASN B 79 -166.06 -76.61 REMARK 500 ARG B 90 -90.70 -155.83 REMARK 500 PRO C 17 89.70 -55.52 REMARK 500 GLN C 20 8.04 154.65 REMARK 500 PRO C 40 155.38 -47.29 REMARK 500 THR C 58 0.21 -57.29 REMARK 500 ASN C 79 -165.83 -76.77 REMARK 500 ARG C 90 -94.01 -157.12 REMARK 500 ASP D 16 60.19 -151.44 REMARK 500 PRO D 17 102.64 -51.03 REMARK 500 GLN D 20 35.50 33.28 REMARK 500 PRO D 40 154.28 -47.36 REMARK 500 THR D 58 22.30 -64.31 REMARK 500 ASP D 59 18.15 -145.81 REMARK 500 ASN D 79 -166.38 -76.29 REMARK 500 ARG D 90 -87.74 -162.10 REMARK 500 TYR D 145 -30.69 -135.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 PRO C 18 48.6 L L OUTSIDE RANGE REMARK 500 ALA C 19 20.2 L L OUTSIDE RANGE 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D1148 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UR6 RELATED DB: PDB REMARK 900 NMR BASED STRUCTURAL MODEL OF THE UBCH5B- REMARK 900 CNOT4 COMPLEX REMARK 900 RELATED ID: 1W4U RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE UBIQUITIN REMARK 900 CONJUGATING ENZYME UBCH5B REMARK 900 RELATED ID: 2CLW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN UBIQUITIN- REMARK 900 CONJUGATING ENZYME UBCH5B REMARK 900 RELATED ID: 2ESK RELATED DB: PDB REMARK 900 HUMAN UBIQUITIN-CONJUGATING ENZYME (E2) UBCH5B REMARK 900 , WILD-TYPE REMARK 900 RELATED ID: 2ESO RELATED DB: PDB REMARK 900 HUMAN UBIQUITIN-CONJUGATING ENZYME (E2) UBCH5B REMARK 900 MUTANTILE37ALA REMARK 900 RELATED ID: 2ESP RELATED DB: PDB REMARK 900 HUMAN UBIQUITIN-CONJUGATING ENZYME (E2) UBCH5B REMARK 900 MUTANTILE88ALA REMARK 900 RELATED ID: 2ESQ RELATED DB: PDB REMARK 900 HUMAN UBIQUITIN-CONJUGATING ENZYME (E2) UBCH5B REMARK 900 MUTANTSER94GLY REMARK 999 REMARK 999 SEQUENCE REMARK 999 IN ADDITION TO THE RGS SEQUENCE PRECEDING THE UNIPROT REMARK 999 UBCH5A SEQUENCE, THE FOLLOWING RESIDUES WERE PRESENT REMARK 999 IN THE STRUCTURE, BUT NOT LOCATED IN THE ELECTRON REMARK 999 DENSITY MAPS,PRESUMABLY DUE TO DISORDER: MKHHHHHHPMSGLVP DBREF 2C4O A -17 0 PDB 2C4O 2C4O -17 0 DBREF 2C4O A 1 147 UNP P62837 UB2D2_HUMAN 1 147 DBREF 2C4O B -17 0 PDB 2C4O 2C4O -17 0 DBREF 2C4O B 1 147 UNP P62837 UB2D2_HUMAN 1 147 DBREF 2C4O C -17 0 PDB 2C4O 2C4O -17 0 DBREF 2C4O C 1 147 UNP P62837 UB2D2_HUMAN 1 147 DBREF 2C4O D -17 0 PDB 2C4O 2C4O -17 0 DBREF 2C4O D 1 147 UNP P62837 UB2D2_HUMAN 1 147 SEQRES 1 A 165 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER GLY LEU SEQRES 2 A 165 VAL PRO ARG GLY SER MET ALA LEU LYS ARG ILE HIS LYS SEQRES 3 A 165 GLU LEU ASN ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SEQRES 4 A 165 SER ALA GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN SEQRES 5 A 165 ALA THR ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY SEQRES 6 A 165 GLY VAL PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR SEQRES 7 A 165 PRO PHE LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE SEQRES 8 A 165 TYR HIS PRO ASN ILE ASN SER ASN GLY SER ILE CME LEU SEQRES 9 A 165 ASP ILE LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SEQRES 10 A 165 SER LYS VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP SEQRES 11 A 165 PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG SEQRES 12 A 165 ILE TYR LYS THR ASP ARG GLU LYS TYR ASN ARG ILE ALA SEQRES 13 A 165 ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 B 165 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER GLY LEU SEQRES 2 B 165 VAL PRO ARG GLY SER MET ALA LEU LYS ARG ILE HIS LYS SEQRES 3 B 165 GLU LEU ASN ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SEQRES 4 B 165 SER ALA GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN SEQRES 5 B 165 ALA THR ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY SEQRES 6 B 165 GLY VAL PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR SEQRES 7 B 165 PRO PHE LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE SEQRES 8 B 165 TYR HIS PRO ASN ILE ASN SER ASN GLY SER ILE CYS LEU SEQRES 9 B 165 ASP ILE LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SEQRES 10 B 165 SER LYS VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP SEQRES 11 B 165 PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG SEQRES 12 B 165 ILE TYR LYS THR ASP ARG GLU LYS TYR ASN ARG ILE ALA SEQRES 13 B 165 ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 C 165 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER GLY LEU SEQRES 2 C 165 VAL PRO ARG GLY SER MET ALA LEU LYS ARG ILE HIS LYS SEQRES 3 C 165 GLU LEU ASN ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SEQRES 4 C 165 SER ALA GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN SEQRES 5 C 165 ALA THR ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY SEQRES 6 C 165 GLY VAL PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR SEQRES 7 C 165 PRO PHE LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE SEQRES 8 C 165 TYR HIS PRO ASN ILE ASN SER ASN GLY SER ILE CYS LEU SEQRES 9 C 165 ASP ILE LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SEQRES 10 C 165 SER LYS VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP SEQRES 11 C 165 PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG SEQRES 12 C 165 ILE TYR LYS THR ASP ARG GLU LYS TYR ASN ARG ILE ALA SEQRES 13 C 165 ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 D 165 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER GLY LEU SEQRES 2 D 165 VAL PRO ARG GLY SER MET ALA LEU LYS ARG ILE HIS LYS SEQRES 3 D 165 GLU LEU ASN ASP LEU ALA ARG ASP PRO PRO ALA GLN CYS SEQRES 4 D 165 SER ALA GLY PRO VAL GLY ASP ASP MET PHE HIS TRP GLN SEQRES 5 D 165 ALA THR ILE MET GLY PRO ASN ASP SER PRO TYR GLN GLY SEQRES 6 D 165 GLY VAL PHE PHE LEU THR ILE HIS PHE PRO THR ASP TYR SEQRES 7 D 165 PRO PHE LYS PRO PRO LYS VAL ALA PHE THR THR ARG ILE SEQRES 8 D 165 TYR HIS PRO ASN ILE ASN SER ASN GLY SER ILE CYS LEU SEQRES 9 D 165 ASP ILE LEU ARG SER GLN TRP SER PRO ALA LEU THR ILE SEQRES 10 D 165 SER LYS VAL LEU LEU SER ILE CYS SER LEU LEU CYS ASP SEQRES 11 D 165 PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU ILE ALA ARG SEQRES 12 D 165 ILE TYR LYS THR ASP ARG GLU LYS TYR ASN ARG ILE ALA SEQRES 13 D 165 ARG GLU TRP THR GLN LYS TYR ALA MET MODRES 2C4O CME A 85 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 85 10 HET SO4 A1148 5 HET GOL A1149 6 HET GOL A1150 6 HET GOL D1148 6 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL FORMUL 1 CME C5 H11 N O3 S2 FORMUL 5 SO4 O4 S 2- FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 HOH *262(H2 O1) HELIX 1 1 GLY A -1 ARG A 15 1 17 HELIX 2 2 LEU A 86 ARG A 90 5 5 HELIX 3 3 THR A 98 ASP A 112 1 15 HELIX 4 4 VAL A 120 ASP A 130 1 11 HELIX 5 5 ASP A 130 TYR A 145 1 16 HELIX 6 6 GLY B -1 ASP B 16 1 18 HELIX 7 7 LEU B 86 ARG B 90 5 5 HELIX 8 8 THR B 98 ASP B 112 1 15 HELIX 9 9 VAL B 120 ASP B 130 1 11 HELIX 10 10 ASP B 130 ALA B 146 1 17 HELIX 11 11 SER C 0 ASP C 16 1 17 HELIX 12 12 LEU C 86 ARG C 90 5 5 HELIX 13 13 THR C 98 ASP C 112 1 15 HELIX 14 14 VAL C 120 ASP C 130 1 11 HELIX 15 15 ASP C 130 TYR C 145 1 16 HELIX 16 16 ARG D -2 ARG D 15 1 18 HELIX 17 17 LEU D 86 ARG D 90 5 5 HELIX 18 18 THR D 98 ASP D 112 1 15 HELIX 19 19 VAL D 120 ASP D 130 1 11 HELIX 20 20 ASP D 130 ALA D 146 1 17 SHEET 1 AA 4 CYS A 21 PRO A 25 0 SHEET 2 AA 4 HIS A 32 MET A 38 -1 O GLN A 34 N GLY A 24 SHEET 3 AA 4 VAL A 49 HIS A 55 -1 O PHE A 50 N ILE A 37 SHEET 4 AA 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 SHEET 1 BA 4 CYS B 21 PRO B 25 0 SHEET 2 BA 4 HIS B 32 MET B 38 -1 O GLN B 34 N GLY B 24 SHEET 3 BA 4 VAL B 49 HIS B 55 -1 O PHE B 50 N ILE B 37 SHEET 4 BA 4 LYS B 66 PHE B 69 -1 O LYS B 66 N HIS B 55 SHEET 1 CA 4 CYS C 21 PRO C 25 0 SHEET 2 CA 4 HIS C 32 MET C 38 -1 O GLN C 34 N GLY C 24 SHEET 3 CA 4 VAL C 49 HIS C 55 -1 O PHE C 50 N ILE C 37 SHEET 4 CA 4 LYS C 66 PHE C 69 -1 O LYS C 66 N HIS C 55 SHEET 1 DA 4 CYS D 21 PRO D 25 0 SHEET 2 DA 4 HIS D 32 MET D 38 -1 O GLN D 34 N GLY D 24 SHEET 3 DA 4 VAL D 49 HIS D 55 -1 O PHE D 50 N ILE D 37 SHEET 4 DA 4 LYS D 66 PHE D 69 -1 O LYS D 66 N HIS D 55 LINK C ILE A 84 N CME A 85 1555 1555 1.33 LINK C CME A 85 N LEU A 86 1555 1555 1.33 CISPEP 1 TYR A 60 PRO A 61 0 0.10 CISPEP 2 TYR B 60 PRO B 61 0 2.52 CISPEP 3 TYR C 60 PRO C 61 0 0.07 CISPEP 4 TYR D 60 PRO D 61 0 0.06 SITE 1 AC1 3 LYS A 133 ARG A 136 HOH A2079 SITE 1 AC2 6 CYS A 111 TYR A 127 ARG A 131 ARG D 5 SITE 2 AC2 6 ALA D 96 THR D 98 SITE 1 AC3 2 LEU A 119 HOH A2047 SITE 1 AC4 5 LYS B 133 ARG B 136 ASN D 11 ARG D 15 SITE 2 AC4 5 HOH D2063 CRYST1 45.585 65.803 101.677 90.00 90.14 90.00 P 1 21 1 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 0.021937 0.000000 0.000054 0.00000 SCALE2 0.000000 0.015197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009835 0.00000 MTRIX1 1 -0.999820 0.007240 -0.017670 22.33517 1 MTRIX2 1 -0.006760 -0.999610 -0.027250 27.01925 1 MTRIX3 1 -0.017860 -0.027130 0.999470 -24.26884 1 MTRIX1 2 0.996090 0.002870 0.088300 -3.92320 1 MTRIX2 2 -0.004040 0.999910 0.013070 -0.24234 1 MTRIX3 2 -0.088250 -0.013370 0.996010 -50.41184 1 MTRIX1 3 0.992730 -0.028480 -0.116980 -18.54609 1 MTRIX2 3 -0.032810 -0.998840 -0.035250 -4.85658 1 MTRIX3 3 -0.115840 0.038830 -0.992510 28.47761 1