HEADER LIGASE 20-MAY-97 1U9B TITLE MURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBC9; COMPND 5 EC: 6.3.2.19; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: MAMMALIAN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-2T KEYWDS UBIQUITIN-CONJUGATING ENZYME, UBIQUITIN-DIRECTED KEYWDS 2 PROTEOLYSIS, CELL CYCLE CONTROL, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR H.TONG,G.HATEBOER,A.PERRAKIS,R.BERNARDS,T.K.SIXMA REVDAT 2 24-FEB-09 1U9B 1 VERSN REVDAT 1 07-JUL-97 1U9B 0 JRNL AUTH H.TONG,G.HATEBOER,A.PERRAKIS,R.BERNARDS,T.K.SIXMA JRNL TITL CRYSTAL STRUCTURE OF MURINE/HUMAN UBC9 PROVIDES JRNL TITL 2 INSIGHT INTO THE VARIABILITY OF THE JRNL TITL 3 UBIQUITIN-CONJUGATING SYSTEM. JRNL REF J.BIOL.CHEM. V. 272 21381 1997 JRNL REFN ISSN 0021-9258 JRNL PMID 9261152 JRNL DOI 10.1074/JBC.272.34.21381 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT V. 5-D REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 12854 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 629 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1850 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 629 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12854 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 29.700 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.015 ; 0.500 ; 1313 REMARK 3 BOND ANGLES (DEGREES) : 1.440 ; 3.000 ; 1764 REMARK 3 TORSION ANGLES (DEGREES) : 16.700; 0.000 ; 769 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.006 ; 2.000 ; 34 REMARK 3 GENERAL PLANES (A) : 0.012 ; 5.000 ; 184 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.640 ; 3.000 ; 1313 REMARK 3 NON-BONDED CONTACTS (A) : 0.011 ; 10.000; 13 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET SCALING REMARK 3 KSOL : 0.80 REMARK 3 BSOL : 228.30 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL V1.0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U9B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-96 REMARK 200 TEMPERATURE (KELVIN) : 281 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.885 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12854 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : 0.41000 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1AAK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG MONOMETHYL ETHER 5000,9% REMARK 280 ISOPROPANOL, 0.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER, PH6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 0.00000 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 17.69500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.97500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.94500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.69500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.97500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.94500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.69500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.97500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.94500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.69500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.97500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.94500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A -1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 12 CD GLU A 12 OE1 -0.067 REMARK 500 GLU A 99 CD GLU A 99 OE2 0.070 REMARK 500 GLU A 143 CD GLU A 143 OE2 0.071 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 100 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 127 CB - CG - OD2 ANGL. DEV. = -5.9 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 PRO A 32 -33.80 -39.12 REMARK 500 HIS A 83 142.89 -173.62 REMARK 500 LYS A 101 -106.75 -114.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: C93 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: UBIQUITIN IS LINKED TO UBC9 VIA CYS 93. DBREF 1U9B A 1 158 UNP P63280 UBE2I_MOUSE 1 158 SEQRES 1 A 160 LEU ASN MET SER GLY ILE ALA LEU SER ARG LEU ALA GLN SEQRES 2 A 160 GLU ARG LYS ALA TRP ARG LYS ASP HIS PRO PHE GLY PHE SEQRES 3 A 160 VAL ALA VAL PRO THR LYS ASN PRO ASP GLY THR MET ASN SEQRES 4 A 160 LEU MET ASN TRP GLU CYS ALA ILE PRO GLY LYS LYS GLY SEQRES 5 A 160 THR PRO TRP GLU GLY GLY LEU PHE LYS LEU ARG MET LEU SEQRES 6 A 160 PHE LYS ASP ASP TYR PRO SER SER PRO PRO LYS CYS LYS SEQRES 7 A 160 PHE GLU PRO PRO LEU PHE HIS PRO ASN VAL TYR PRO SER SEQRES 8 A 160 GLY THR VAL CYS LEU SER ILE LEU GLU GLU ASP LYS ASP SEQRES 9 A 160 TRP ARG PRO ALA ILE THR ILE LYS GLN ILE LEU LEU GLY SEQRES 10 A 160 ILE GLN GLU LEU LEU ASN GLU PRO ASN ILE GLN ASP PRO SEQRES 11 A 160 ALA GLN ALA GLU ALA TYR THR ILE TYR CYS GLN ASN ARG SEQRES 12 A 160 VAL GLU TYR GLU LYS ARG VAL ARG ALA GLN ALA LYS LYS SEQRES 13 A 160 PHE ALA PRO SER FORMUL 2 HOH *96(H2 O) HELIX 1 1 MET A 1 LYS A 18 5 18 HELIX 2 2 SER A 95 LEU A 97 5 3 HELIX 3 3 ILE A 109 ASN A 121 1 13 HELIX 4 4 ALA A 131 GLN A 139 1 9 HELIX 5 5 ARG A 141 LYS A 154 1 14 SHEET 1 A 4 LYS A 74 PHE A 77 0 SHEET 2 A 4 LEU A 57 LEU A 63 -1 N LEU A 63 O LYS A 74 SHEET 3 A 4 MET A 36 PRO A 46 -1 N ILE A 45 O PHE A 58 SHEET 4 A 4 VAL A 25 LYS A 30 -1 N THR A 29 O ASN A 37 CISPEP 1 TYR A 68 PRO A 69 0 9.64 CISPEP 2 GLU A 78 PRO A 79 0 -1.13 SITE 1 C93 1 CYS A 93 CRYST1 35.390 93.950 115.890 90.00 90.00 90.00 I 2 2 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 0.028257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008629 0.00000 MASTER 264 0 0 5 4 0 1 6 0 0 0 13 END