HEADER LIGASE 10-MAY-99 1QCQ TITLE UBIQUITIN CONJUGATING ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (UBIQUITIN CONJUGATING ENZYME); COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.19 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS UBIQUITIN, UBIQUITIN-CONJUGATING ENZYME, YEAST, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR W.J.COOK,L.C.JEFFREY,Y.XU,V.CHAU REVDAT 5 14-FEB-24 1QCQ 1 REMARK REVDAT 4 04-OCT-17 1QCQ 1 REMARK REVDAT 3 24-FEB-09 1QCQ 1 VERSN REVDAT 2 06-MAR-00 1QCQ 1 HEADER COMPND REMARK REVDAT 1 17-MAY-99 1QCQ 0 SPRSDE 17-MAY-99 1QCQ 2UCE JRNL AUTH W.J.COOK,L.C.JEFFREY,Y.XU,V.CHAU JRNL TITL TERTIARY STRUCTURES OF CLASS I UBIQUITIN-CONJUGATING ENZYMES JRNL TITL 2 ARE HIGHLY CONSERVED: CRYSTAL STRUCTURE OF YEAST UBC4. JRNL REF BIOCHEMISTRY V. 32 13809 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8268156 JRNL DOI 10.1021/BI00213A009 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 5624 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) : 0.240 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 325 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 686 REMARK 3 BIN R VALUE (WORKING SET) : 0.4090 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 48 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.049 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1161 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) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.47 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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) : 1.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.730 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.440 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.650 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 25.84 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.PA REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000009080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-92; 17-DEC-92; 20-JAN-93; REMARK 200 22-JAN-93 REMARK 200 TEMPERATURE (KELVIN) : 295.0; NULL; NULL; NULL REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N; N; N REMARK 200 RADIATION SOURCE : ROTATING ANODE; NULL; NULL; NULL REMARK 200 BEAMLINE : NULL; NULL; NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300; NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; NULL; NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR; AREA DETECTOR; REMARK 200 AREA DETECTOR; AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : NICOLET; NICOLET; NICOLET; REMARK 200 NICOLET REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5940 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, REMARK 280 CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 45.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.45000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.95000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.45000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 68.85000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.95000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 68.85000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.90000 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 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 GLU A 15 -8.41 -56.50 REMARK 500 ARG A 16 -76.20 -113.41 REMARK 500 THR A 20 -61.90 -93.12 REMARK 500 SER A 23 115.45 -165.49 REMARK 500 ASP A 43 44.60 -93.42 REMARK 500 LYS A 91 -108.89 -142.45 REMARK 500 ALA A 114 -177.88 -58.99 REMARK 500 PRO A 119 76.46 -58.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UCE RELATED DB: PDB REMARK 900 THIS ENTRY UPDATES 2UCE DBREF 1QCQ A 1 148 UNP P15731 UBC4_YEAST 1 148 SEQRES 1 A 148 MET SER SER SER LYS ARG ILE ALA LYS GLU LEU SER ASP SEQRES 2 A 148 LEU GLU ARG ASP PRO PRO THR SER CYS SER ALA GLY PRO SEQRES 3 A 148 VAL GLY ASP ASP LEU TYR HIS TRP GLN ALA SER ILE MET SEQRES 4 A 148 GLY PRO ALA ASP SER PRO TYR ALA GLY GLY VAL PHE PHE SEQRES 5 A 148 LEU SER ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO SEQRES 6 A 148 PRO LYS ILE SER PHE THR THR LYS ILE TYR HIS PRO ASN SEQRES 7 A 148 ILE ASN ALA ASN GLY ASN ILE CYS LEU ASP ILE LEU LYS SEQRES 8 A 148 ASP GLN TRP SER PRO ALA LEU THR LEU SER LYS VAL LEU SEQRES 9 A 148 LEU SER ILE CYS SER LEU LEU THR ASP ALA ASN PRO ASP SEQRES 10 A 148 ASP PRO LEU VAL PRO GLU ILE ALA HIS ILE TYR LYS THR SEQRES 11 A 148 ASP ARG PRO LYS TYR GLU ALA THR ALA ARG GLU TRP THR SEQRES 12 A 148 LYS LYS TYR ALA VAL HELIX 1 1 MET A 1 ARG A 16 1 16 HELIX 2 2 LEU A 87 LYS A 91 5 5 HELIX 3 3 THR A 99 ASP A 113 1 15 HELIX 4 4 VAL A 121 ASP A 131 1 11 HELIX 5 5 ASP A 131 ALA A 147 1 17 SHEET 1 A 4 CYS A 22 VAL A 27 0 SHEET 2 A 4 ASP A 30 MET A 39 -1 N ASP A 30 O VAL A 27 SHEET 3 A 4 VAL A 50 HIS A 56 -1 N PHE A 51 O ILE A 38 SHEET 4 A 4 LYS A 67 PHE A 70 -1 N LYS A 67 O HIS A 56 CISPEP 1 TYR A 61 PRO A 62 0 0.19 CRYST1 66.900 66.900 91.800 90.00 90.00 90.00 P 41 21 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 0.014948 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010893 0.00000