HEADER UBIQUITIN CONJUGATION 07-NOV-96 1UCZ OBSLTE 18-MAR-98 1UCZ 2UCZ TITLE UBIQUITIN CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES TITLE 2 CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CONJUGATING ENZYME; COMPND 3 CHAIN: NULL; COMPND 4 SYNONYM: UBC7; COMPND 5 EC: 6.3.2.19; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 CELLULAR_LOCATION: CYTOPLASM; SOURCE 5 GENE: UBC7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS UBIQUITIN CONJUGATION, LIGASE, YEAST EXPDTA X-RAY DIFFRACTION AUTHOR W.J.COOK,V.CHAU REVDAT 1 15-MAY-97 1UCZ 0 JRNL AUTH W.J.COOK,P.D.MARTIN,B.F.EDWARDS,R.K.YAMAZAKI,V.CHAU JRNL TITL CRYSTAL STRUCTURE OF A CLASS I UBIQUITIN JRNL TITL 2 CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES JRNL TITL 3 CEREVISIAE AT 2.9 ANGSTROMS RESOLUTION JRNL REF BIOCHEMISTRY V. 36 1621 1997 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.85 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 77.2 REMARK 3 NUMBER OF REFLECTIONS : 4997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 2.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.10 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 30.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 322 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1289 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) : 25.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.30 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.39 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.94 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) : 1.650 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.620 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.110 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.670 ; 2.000 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UCZ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 RESIDUES 1 AND 2 WERE NOT IDENTIFIED. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-1994 REMARK 200 TEMPERATURE (KELVIN) : 295.0 REMARK 200 PH : 7.40 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : MULTIWIRE REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6557 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.930 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15400 REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32700 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1AAK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X-Y,X,5/6+Z REMARK 290 3555 -Y,X-Y,2/3+Z REMARK 290 4555 -X,-Y,1/2+Z REMARK 290 5555 -X+Y,-X,1/3+Z REMARK 290 6555 Y,-X+Y,1/6+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 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.08333 REMARK 290 SMTRY1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.86667 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 24.65000 REMARK 290 SMTRY1 5 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.43333 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.21667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). 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 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 1 REMARK 465 SER 2 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO 65 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 PHE 73 N - CA - C ANGL. DEV. =-13.6 DEGREES REMARK 500 PRO 75 C - N - CA ANGL. DEV. =-14.6 DEGREES REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: KABSCH AND SANDER REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: KABSCH AND SANDER REMARK 750 REMARK 750 TURN REMARK 750 DETERMINATION METHOD: AUTHOR-DETERMINED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: S1 REMARK 800 SITE_DESCRIPTION: UBIQUITIN-ACCEPTING RESIDUE. REMARK 850 REMARK 850 CORRECTION BEFORE RELEASE REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE REMARK 850 DATE REVISED: 02-DEC-1996 TRACKING NUMBER: T9952 REMARK 999 REMARK 999 SEQUENCE REMARK 999 1UCZ SWS Q02159 1 - 2 NOT IN ATOMS LIST DBREF 1UCZ 3 165 UNP Q02159 UBC7_YEAST 3 165 SEQRES 1 165 MET SER LYS THR ALA GLN LYS ARG LEU LEU LYS GLU LEU SEQRES 2 165 GLN GLN LEU ILE LYS ASP SER PRO PRO GLY ILE VAL ALA SEQRES 3 165 GLY PRO LYS SER GLU ASN ASN ILE PHE ILE TRP ASP CYS SEQRES 4 165 LEU ILE GLN GLY PRO PRO ASP THR PRO TYR ALA ASP GLY SEQRES 5 165 VAL PHE ASN ALA LYS LEU GLU PHE PRO LYS ASP TYR PRO SEQRES 6 165 LEU SER PRO PRO LYS LEU THR PHE THR PRO SER ILE LEU SEQRES 7 165 HIS PRO ASN ILE TYR PRO ASN GLY GLU VAL CYS ILE SER SEQRES 8 165 ILE LEU HIS SER PRO GLY ASP ASP PRO ASN MET TYR GLU SEQRES 9 165 LEU ALA GLU GLU ARG TRP SER PRO VAL GLN SER VAL GLU SEQRES 10 165 LYS ILE LEU LEU SER VAL MET SER MET LEU SER GLU PRO SEQRES 11 165 ASN ILE GLU SER GLY ALA ASN ILE ASP ALA CYS ILE LEU SEQRES 12 165 TRP ARG ASP ASN ARG PRO GLU PHE GLU ARG GLN VAL LYS SEQRES 13 165 LEU SER ILE LEU LYS SER LEU GLY PHE HELIX 1 1 LYS 7 LEU 13 1 7 HELIX 2 2 SER 91 LEU 93 5 3 HELIX 3 3 GLU 104 GLU 108 5 5 HELIX 4 4 VAL 116 SER 128 1 13 HELIX 5 5 ILE 132 SER 134 5 3 HELIX 6 6 ILE 138 ASP 146 1 9 HELIX 7 7 ARG 148 SER 162 1 15 SHEET 1 A 4 ILE 24 GLY 27 0 SHEET 2 A 4 ILE 36 GLN 42 -1 N LEU 40 O VAL 25 SHEET 3 A 4 VAL 53 GLU 59 -1 N LEU 58 O TRP 37 SHEET 4 A 4 LEU 71 PHE 73 -1 N THR 72 O LYS 57 TURN 1 1 TYR 64 SER 67 TYPE VIA CISPEP 1 TYR 64 PRO 65 0 -0.76 SITE 1 S1 1 CYS 89 CRYST1 106.500 106.500 49.300 90.00 90.00 120.00 P 65 6 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 0.009390 0.005421 0.000000 0.00000 SCALE2 0.000000 0.010842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020284 0.00000