PDB Short entry for 2UCZ HEADER UBIQUITIN CONJUGATION 07-NOV-97 2UCZ TITLE UBIQUITIN CONJUGATING ENZYME (UBC7) FROM SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CONJUGATING ENZYME; COMPND 3 CHAIN: A; 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 ORGANISM_TAXID: 4932; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: UBC7; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN CONJUGATION, LIGASE, YEAST EXPDTA X-RAY DIFFRACTION AUTHOR W.J.COOK,V.CHAU REVDAT 3 09-AUG-23 2UCZ 1 REMARK REVDAT 2 24-FEB-09 2UCZ 1 VERSN REVDAT 1 18-MAR-98 2UCZ 0 SPRSDE 18-MAR-98 2UCZ 1UCZ 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 CONJUGATING ENZYME JRNL TITL 2 (UBC7) FROM SACCHAROMYCES CEREVISIAE AT 2.9 ANGSTROMS JRNL TITL 3 RESOLUTION. JRNL REF BIOCHEMISTRY V. 36 1621 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9048545 JRNL DOI 10.1021/BI962639E REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 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) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 6255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : A POSTERIORI 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 (%) : 5.700 REMARK 3 FREE R VALUE TEST SET COUNT : 354 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 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) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 462 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 35 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.058 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1295 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) : 28.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.10 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) : 0.37 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.71 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.510 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2UCZ 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_1000178718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-94 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R 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 : AREA DETECTOR 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 3.851 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: PROTEIN WAS CRYSTALLIZED FROM 0.6 M REMARK 280 SODIUM CITRATE, 100 MM HEPES, PH 7.4, USING HANGING DROP REMARK 280 TECHNIQUE AT 23 DEG, VAPOR DIFFUSION - HANGING DROP, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 32.86667 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 16.43333 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 8.21667 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 41.08333 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 MET A 1 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 PRO A 45 C - N - CA ANGL. DEV. = 9.5 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 ASP A 19 63.97 -112.15 REMARK 500 PRO A 48 3.34 -62.99 REMARK 500 ALA A 50 -52.02 -25.76 REMARK 500 THR A 74 -71.92 -50.81 REMARK 500 PRO A 100 1.37 -56.97 REMARK 500 GLU A 104 -85.28 -59.79 REMARK 500 LEU A 105 -54.07 -4.82 REMARK 500 ALA A 106 -87.48 -2.46 REMARK 500 PRO A 112 -6.14 -50.73 REMARK 500 ARG A 145 -72.15 -67.14 REMARK 500 ASP A 146 -73.38 -65.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: C89 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: UBIQUITIN-ACCEPTING RESIDUE. DBREF 2UCZ A 1 165 UNP Q02159 UBC7_YEAST 1 165 SEQRES 1 A 165 MET SER LYS THR ALA GLN LYS ARG LEU LEU LYS GLU LEU SEQRES 2 A 165 GLN GLN LEU ILE LYS ASP SER PRO PRO GLY ILE VAL ALA SEQRES 3 A 165 GLY PRO LYS SER GLU ASN ASN ILE PHE ILE TRP ASP CYS SEQRES 4 A 165 LEU ILE GLN GLY PRO PRO ASP THR PRO TYR ALA ASP GLY SEQRES 5 A 165 VAL PHE ASN ALA LYS LEU GLU PHE PRO LYS ASP TYR PRO SEQRES 6 A 165 LEU SER PRO PRO LYS LEU THR PHE THR PRO SER ILE LEU SEQRES 7 A 165 HIS PRO ASN ILE TYR PRO ASN GLY GLU VAL CYS ILE SER SEQRES 8 A 165 ILE LEU HIS SER PRO GLY ASP ASP PRO ASN MET TYR GLU SEQRES 9 A 165 LEU ALA GLU GLU ARG TRP SER PRO VAL GLN SER VAL GLU SEQRES 10 A 165 LYS ILE LEU LEU SER VAL MET SER MET LEU SER GLU PRO SEQRES 11 A 165 ASN ILE GLU SER GLY ALA ASN ILE ASP ALA CYS ILE LEU SEQRES 12 A 165 TRP ARG ASP ASN ARG PRO GLU PHE GLU ARG GLN VAL LYS SEQRES 13 A 165 LEU SER ILE LEU LYS SER LEU GLY PHE HELIX 1 1 LYS A 3 LYS A 18 1 16 HELIX 2 2 SER A 91 LEU A 93 5 3 HELIX 3 3 VAL A 116 SER A 128 1 13 HELIX 4 4 ILE A 132 SER A 134 5 3 HELIX 5 5 ILE A 138 ARG A 145 1 8 HELIX 6 6 ARG A 148 LEU A 163 1 16 SHEET 1 A 4 ILE A 24 PRO A 28 0 SHEET 2 A 4 ILE A 36 GLN A 42 -1 N LEU A 40 O VAL A 25 SHEET 3 A 4 VAL A 53 GLU A 59 -1 N LEU A 58 O TRP A 37 SHEET 4 A 4 LYS A 70 PHE A 73 -1 N THR A 72 O LYS A 57 CISPEP 1 TYR A 64 PRO A 65 0 0.42 SITE 1 C89 1 CYS A 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