PDB Short entry for 1U9A HEADER UBIQUITIN-CONJUGATING ENZYME 11-FEB-97 1U9A TITLE HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.19; COMPND 5 ENGINEERED: YES 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 KEYWDS UBIQUITIN-CONJUGATING ENZYME, UBIQUITIN-DIRECTED PROTEOLYSIS, CELL KEYWDS 2 CYCLE CONTROL, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR H.TONG,G.HATEBOER,A.PERRAKIS,R.BERNARDS,T.K.SIXMA REVDAT 3 09-AUG-23 1U9A 1 REMARK REVDAT 2 24-FEB-09 1U9A 1 VERSN REVDAT 1 15-MAY-97 1U9A 0 JRNL AUTH H.TONG,G.HATEBOER,A.PERRAKIS,R.BERNARDS,T.K.SIXMA JRNL TITL CRYSTAL STRUCTURE OF MURINE/HUMAN UBC9 PROVIDES INSIGHT INTO JRNL TITL 2 THE VARIABILITY OF THE 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 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E 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 (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 11707 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) : 0.160 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 : 587 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) : 0.1600 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.00 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 587 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11707 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1283 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 25.100 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; 0.500 ; 1320 REMARK 3 BOND ANGLES (DEGREES) : 1.289 ; 3.000 ; 1774 REMARK 3 TORSION ANGLES (DEGREES) : 15.229; 0.000 ; 774 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.007 ; 2.000 ; 33 REMARK 3 GENERAL PLANES (A) : 0.011 ; 5.000 ; 185 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.435 ; 3.000 ; 1320 REMARK 3 NON-BONDED CONTACTS (A) : 0.068 ; 10.000; 20 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 : 259.4 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 1U9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176897. 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 : 7.5 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 : BW7B 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 : 12295 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : 0.12000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : 0.42000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 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 (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED IN THE SPACE REMARK 280 GROUP P21 FROM 9% PEG 4000, 9% ISOPROPANOL, 0.1 M HEPES, PH 7.5 REMARK 280 SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: P 21: X, Y,Z -X,Y+ REMARK 280 1/2,-Z 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 17.59000 REMARK 290 SMTRY3 2 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: 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 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 SER A 158 O 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 O LYS A 30 O HOH A 245 2.02 REMARK 500 REMARK 500 REMARK: NULL 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 54 CD GLU A 54 OE2 0.068 REMARK 500 GLU A 122 CD GLU A 122 OE2 0.073 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 19 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 33 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 100 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 127 CB - CG - OD1 ANGL. DEV. = -5.7 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 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 HIS A 83 137.02 -173.26 REMARK 500 LYS A 101 -109.61 -110.28 REMARK 500 ASN A 140 95.08 -160.37 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: CYS 93 IS THE CONSERVED UBIQUITIN-ACCEPTING REMARK 800 CYSTEINE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES WITH RESIDUE NUMBERS BELOW 1 ARE CLONING REMARK 999 ARTIFACTS. DBREF 1U9A 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 *103(H2 O) HELIX 1 1 MET A 1 LYS A 18 1 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 PHE A 155 1 15 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 8.96 CISPEP 2 GLU A 78 PRO A 79 0 3.16 SITE 1 C93 2 CYS A 93 ASN A 0 CRYST1 52.040 35.180 58.100 90.00 111.20 90.00 P 1 21 1 2 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 0.019216 0.000000 0.007453 0.00000 SCALE2 0.000000 0.028425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018461 0.00000