PDB Short entry for 1FZY HEADER LIGASE 04-OCT-00 1FZY TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE UBIQUITIN CONJUGATING TITLE 2 ENZYME 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.3.2.19; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-BETA ROLL, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GLOVER,R.S.WILLIAMS REVDAT 3 21-JUL-21 1FZY 1 REMARK SHEET REVDAT 2 24-FEB-09 1FZY 1 VERSN REVDAT 1 04-OCT-01 1FZY 0 JRNL AUTH K.S.HAMILTON,M.J.ELLISON,K.R.BARBER,R.S.WILLIAMS,J.T.HUZIL, JRNL AUTH 2 S.MCKENNA,C.PTAK,M.GLOVER,G.S.SHAW JRNL TITL STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER JRNL TITL 2 INTERMEDIATE REVEALS A NOVEL ROLE FOR THE UBIQUITIN TAIL. JRNL REF STRUCTURE V. 9 897 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11591345 JRNL DOI 10.1016/S0969-2126(01)00657-8 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 (CNS) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 23274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2301 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL 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 : 2313 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.274 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 0.872 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FZY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2030 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000-MONOMETHYLETHER, AMMONIUM REMARK 280 SULPHATE, ISOPROPANOL, MES BUFFER, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K 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 23.73550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER. A NON- REMARK 300 CRYSTALLOGRAPHICALLY RELATED DIMER IS FOUND IN THE ASYMMETRIC UNIT. REMARK 300 THE SIGNIFICANCE OF THIS DIMER INTERACTION IS UNKNOWN. THE REMARK 300 BIOLOGICAL ASSEMBLY IS A MONOMER. A NON-CRYSTALLOGRAPHICALLY REMARK 300 RELATED DIMER IS FOUND IN THE ASYMMETRIC UNIT. THE SIGNIFICANCE OF REMARK 300 THIS DIMER INTERACTION IS UNKNOWN. 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 LYS A 5 CG CD CE NZ REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 ASP A 90 CG OD1 OD2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 GLU A 135 CG CD OE1 OE2 REMARK 470 ARG B 3 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 GLU B 57 CG CD OE1 OE2 REMARK 470 LYS B 93 CG CD CE NZ 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 B 118 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 PRO B 121 C - N - CA ANGL. DEV. = 11.3 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 LYS A 93 -93.26 -115.69 REMARK 500 GLU A 117 77.86 -117.33 REMARK 500 LYS B 93 -88.24 -110.96 REMARK 500 ASP B 133 83.79 -154.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 1FZY A 2 150 UNP P21734 UBC1_YEAST 2 150 DBREF 1FZY B 2 150 UNP P21734 UBC1_YEAST 2 150 SEQRES 1 A 149 SER ARG ALA LYS ARG ILE MET LYS GLU ILE GLN ALA VAL SEQRES 2 A 149 LYS ASP ASP PRO ALA ALA HIS ILE THR LEU GLU PHE VAL SEQRES 3 A 149 SER GLU SER ASP ILE HIS HIS LEU LYS GLY THR PHE LEU SEQRES 4 A 149 GLY PRO PRO GLY THR PRO TYR GLU GLY GLY LYS PHE VAL SEQRES 5 A 149 VAL ASP ILE GLU VAL PRO MET GLU TYR PRO PHE LYS PRO SEQRES 6 A 149 PRO LYS MET GLN PHE ASP THR LYS VAL TYR HIS PRO ASN SEQRES 7 A 149 ILE SER SER VAL THR GLY ALA ILE CYS LEU ASP ILE LEU SEQRES 8 A 149 LYS ASN ALA TRP SER PRO VAL ILE THR LEU LYS SER ALA SEQRES 9 A 149 LEU ILE SER LEU GLN ALA LEU LEU GLN SER PRO GLU PRO SEQRES 10 A 149 ASN ASP PRO GLN ASP ALA GLU VAL ALA GLN HIS TYR LEU SEQRES 11 A 149 ARG ASP ARG GLU SER PHE ASN LYS THR ALA ALA LEU TRP SEQRES 12 A 149 THR ARG LEU TYR ALA SER SEQRES 1 B 149 SER ARG ALA LYS ARG ILE MET LYS GLU ILE GLN ALA VAL SEQRES 2 B 149 LYS ASP ASP PRO ALA ALA HIS ILE THR LEU GLU PHE VAL SEQRES 3 B 149 SER GLU SER ASP ILE HIS HIS LEU LYS GLY THR PHE LEU SEQRES 4 B 149 GLY PRO PRO GLY THR PRO TYR GLU GLY GLY LYS PHE VAL SEQRES 5 B 149 VAL ASP ILE GLU VAL PRO MET GLU TYR PRO PHE LYS PRO SEQRES 6 B 149 PRO LYS MET GLN PHE ASP THR LYS VAL TYR HIS PRO ASN SEQRES 7 B 149 ILE SER SER VAL THR GLY ALA ILE CYS LEU ASP ILE LEU SEQRES 8 B 149 LYS ASN ALA TRP SER PRO VAL ILE THR LEU LYS SER ALA SEQRES 9 B 149 LEU ILE SER LEU GLN ALA LEU LEU GLN SER PRO GLU PRO SEQRES 10 B 149 ASN ASP PRO GLN ASP ALA GLU VAL ALA GLN HIS TYR LEU SEQRES 11 B 149 ARG ASP ARG GLU SER PHE ASN LYS THR ALA ALA LEU TRP SEQRES 12 B 149 THR ARG LEU TYR ALA SER FORMUL 3 HOH *283(H2 O) HELIX 1 1 SER A 2 ASP A 16 1 15 HELIX 2 2 ASP A 17 ALA A 20 5 4 HELIX 3 4 THR A 101 SER A 115 1 15 HELIX 4 5 ASP A 123 ASP A 133 1 11 HELIX 5 6 ASP A 133 ALA A 149 1 17 HELIX 6 7 SER B 2 ASP B 16 1 15 HELIX 7 8 ASP B 17 HIS B 21 5 5 HELIX 8 10 THR B 101 SER B 115 1 15 HELIX 9 11 ASP B 123 ASP B 133 1 11 HELIX 10 12 ASP B 133 SER B 150 1 18 SHEET 1 A 3 ILE A 22 PHE A 26 0 SHEET 2 A 3 HIS A 34 LEU A 40 -1 N LYS A 36 O GLU A 25 SHEET 3 A 3 LYS A 51 GLU A 57 -1 N PHE A 52 O PHE A 39 SHEET 1 B 3 THR B 23 PHE B 26 0 SHEET 2 B 3 HIS B 34 LEU B 40 -1 N LYS B 36 O GLU B 25 SHEET 3 B 3 LYS B 68 PHE B 71 -1 CISPEP 1 TYR A 62 PRO A 63 0 0.63 CISPEP 2 TYR B 62 PRO B 63 0 -0.16 CRYST1 42.166 47.471 75.776 90.00 92.62 90.00 P 1 21 1 4 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 0.023716 0.000000 0.001085 0.00000 SCALE2 0.000000 0.021065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013211 0.00000