HEADER LIGASE 31-MAY-01 1JAT TITLE MMS2/UBC13 UBIQUITIN CONJUGATING ENZYME COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17.5 KDA; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.19; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN-CONJUGATING ENZYME VARIANT MMS2; COMPND 8 CHAIN: B; COMPND 9 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 GENE: UBC13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21PJY2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: MMS2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21PJY2; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS UBIQUITIN, UBIQUITIN-CONJUGATING ENZYME, E2, UEV, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.P.VANDEMARK,R.M.HOFMANN,C.TSUI,C.M.PICKART,C.WOLBERGER REVDAT 4 07-FEB-24 1JAT 1 SEQADV REVDAT 3 24-FEB-09 1JAT 1 VERSN REVDAT 2 01-APR-03 1JAT 1 JRNL REVDAT 1 20-JUN-01 1JAT 0 JRNL AUTH A.P.VANDEMARK,R.M.HOFMANN,C.TSUI,C.M.PICKART,C.WOLBERGER JRNL TITL MOLECULAR INSIGHTS INTO POLYUBIQUITIN CHAIN ASSEMBLY: JRNL TITL 2 CRYSTAL STRUCTURE OF THE MMS2/UBC13 HETERODIMER. JRNL REF CELL(CAMBRIDGE,MASS.) V. 105 711 2001 JRNL REFN ISSN 0092-8674 JRNL PMID 11440714 JRNL DOI 10.1016/S0092-8674(01)00387-7 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1023636.200 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 36093 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) : 0.203 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1810 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4144 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 211 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.96000 REMARK 3 B22 (A**2) : -1.57000 REMARK 3 B33 (A**2) : -0.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.280 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 66.72 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.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1JAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9115 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, TRIS, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 31.89850 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLU A 153 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLY B 20 REMARK 465 PHE B 21 REMARK 465 GLY B 22 REMARK 465 PRO B 23 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 GLU A 13 CG CD OE1 OE2 REMARK 470 ASP A 29 CG OD1 OD2 REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 GLU B 54 CG CD OE1 OE2 REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 LYS B 127 CG CD CE NZ REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 GLU B 133 CG CD OE1 OE2 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 92 -134.51 -113.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JAT A 2 153 UNP P52490 UBC13_YEAST 2 153 DBREF 1JAT B 1 137 UNP P53152 MMS2_YEAST 1 137 SEQADV 1JAT GLY A -1 UNP P52490 CLONING ARTIFACT SEQADV 1JAT SER A 0 UNP P52490 CLONING ARTIFACT SEQADV 1JAT ALA A 1 UNP P52490 CLONING ARTIFACT SEQADV 1JAT HIS B 0 UNP P53152 EXPRESSION TAG SEQRES 1 A 155 GLY SER ALA ALA SER LEU PRO LYS ARG ILE ILE LYS GLU SEQRES 2 A 155 THR GLU LYS LEU VAL SER ASP PRO VAL PRO GLY ILE THR SEQRES 3 A 155 ALA GLU PRO HIS ASP ASP ASN LEU ARG TYR PHE GLN VAL SEQRES 4 A 155 THR ILE GLU GLY PRO GLU GLN SER PRO TYR GLU ASP GLY SEQRES 5 A 155 ILE PHE GLU LEU GLU LEU TYR LEU PRO ASP ASP TYR PRO SEQRES 6 A 155 MET GLU ALA PRO LYS VAL ARG PHE LEU THR LYS ILE TYR SEQRES 7 A 155 HIS PRO ASN ILE ASP ARG LEU GLY ARG ILE CYS LEU ASP SEQRES 8 A 155 VAL LEU LYS THR ASN TRP SER PRO ALA LEU GLN ILE ARG SEQRES 9 A 155 THR VAL LEU LEU SER ILE GLN ALA LEU LEU ALA SER PRO SEQRES 10 A 155 ASN PRO ASN ASP PRO LEU ALA ASN ASP VAL ALA GLU ASP SEQRES 11 A 155 TRP ILE LYS ASN GLU GLN GLY ALA LYS ALA LYS ALA ARG SEQRES 12 A 155 GLU TRP THR LYS LEU TYR ALA LYS LYS LYS PRO GLU SEQRES 1 B 138 HIS MET SER LYS VAL PRO ARG ASN PHE ARG LEU LEU GLU SEQRES 2 B 138 GLU LEU GLU LYS GLY GLU LYS GLY PHE GLY PRO GLU SER SEQRES 3 B 138 CYS SER TYR GLY LEU ALA ASP SER ASP ASP ILE THR MET SEQRES 4 B 138 THR LYS TRP ASN GLY THR ILE LEU GLY PRO PRO HIS SER SEQRES 5 B 138 ASN HIS GLU ASN ARG ILE TYR SER LEU SER ILE ASP CYS SEQRES 6 B 138 GLY PRO ASN TYR PRO ASP SER PRO PRO LYS VAL THR PHE SEQRES 7 B 138 ILE SER LYS ILE ASN LEU PRO CYS VAL ASN PRO THR THR SEQRES 8 B 138 GLY GLU VAL GLN THR ASP PHE HIS THR LEU ARG ASP TRP SEQRES 9 B 138 LYS ARG ALA TYR THR MET GLU THR LEU LEU LEU ASP LEU SEQRES 10 B 138 ARG LYS GLU MET ALA THR PRO ALA ASN LYS LYS LEU ARG SEQRES 11 B 138 GLN PRO LYS GLU GLY GLU THR PHE FORMUL 3 HOH *276(H2 O) HELIX 1 1 PRO A 5 ASP A 18 1 14 HELIX 2 2 LEU A 88 LYS A 92 5 5 HELIX 3 3 GLN A 100 SER A 114 1 15 HELIX 4 4 VAL A 125 ASN A 132 1 8 HELIX 5 5 ASN A 132 ALA A 148 1 17 HELIX 6 6 PRO B 5 LYS B 19 1 15 HELIX 7 7 PHE B 97 ASP B 102 1 6 HELIX 8 8 THR B 108 ALA B 121 1 14 HELIX 9 9 THR B 122 LYS B 127 1 6 SHEET 1 A 4 ILE A 23 HIS A 28 0 SHEET 2 A 4 ASN A 31 GLU A 40 -1 N ASN A 31 O HIS A 28 SHEET 3 A 4 GLY A 50 TYR A 57 -1 N PHE A 52 O ILE A 39 SHEET 4 A 4 LYS A 68 PHE A 71 -1 N LYS A 68 O TYR A 57 SHEET 1 B 4 ILE A 23 HIS A 28 0 SHEET 2 B 4 ASN A 31 GLU A 40 -1 N ASN A 31 O HIS A 28 SHEET 3 B 4 GLY A 50 TYR A 57 -1 N PHE A 52 O ILE A 39 SHEET 4 B 4 LYS A 149 LYS A 150 -1 N LYS A 149 O ILE A 51 SHEET 1 C 4 CYS B 26 LEU B 30 0 SHEET 2 C 4 LYS B 40 LEU B 46 -1 N ASN B 42 O GLY B 29 SHEET 3 C 4 ILE B 57 ASP B 63 -1 N TYR B 58 O ILE B 45 SHEET 4 C 4 LYS B 74 PHE B 77 -1 O LYS B 74 N ASP B 63 CISPEP 1 TYR A 62 PRO A 63 0 1.06 CISPEP 2 TYR B 68 PRO B 69 0 0.48 CRYST1 43.158 63.797 53.152 90.00 105.83 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 0.023171 0.000000 0.006570 0.00000 SCALE2 0.000000 0.015675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019556 0.00000