HEADER SIGNALING PROTEIN 24-JUL-17 5OJW TITLE S. CEREVISIAE UBC13 - MMS2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 13; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME 13,UBIQUITIN CARRIER PROTEIN COMPND 5 13,UBIQUITIN-PROTEIN LIGASE 13; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN-CONJUGATING ENZYME VARIANT MMS2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: UEV MMS2; COMPND 12 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 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: UBC13, YDR092W, YD6652.04; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 STRAIN: ATCC 204508 / S288C; SOURCE 14 GENE: MMS2, YGL087C; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS E2, UBIQUITIN, COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.SHARON,R.RATHI,O.LEVIN-KRAVETS,I.ATTALI,G.PRAG REVDAT 2 17-JAN-24 5OJW 1 REMARK REVDAT 1 02-AUG-17 5OJW 0 JRNL AUTH I.SHARON,R.RATHI,O.LEVIN-KRAVETS,I.ATTALI,G.PRAG JRNL TITL S. CEREVISIAE UBC13 - MMS2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 20979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.7921 - 3.8252 0.97 3013 157 0.1583 0.1843 REMARK 3 2 3.8252 - 3.0364 0.98 2863 148 0.1446 0.1781 REMARK 3 3 3.0364 - 2.6526 0.97 2834 154 0.1629 0.2080 REMARK 3 4 2.6526 - 2.4101 0.98 2834 150 0.1611 0.2632 REMARK 3 5 2.4101 - 2.2374 0.98 2822 151 0.1589 0.1988 REMARK 3 6 2.2374 - 2.1054 0.98 2798 127 0.1729 0.2450 REMARK 3 7 2.1054 - 2.0000 0.98 2786 142 0.2076 0.2739 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.350 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 2523 REMARK 3 ANGLE : 1.035 3450 REMARK 3 CHIRALITY : 0.057 371 REMARK 3 PLANARITY : 0.008 460 REMARK 3 DIHEDRAL : 20.397 1595 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OJW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.070989 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29813 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.773 REMARK 200 RESOLUTION RANGE LOW (A) : 45.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 1JAT REMARK 200 REMARK 200 REMARK: 1-2 MM LONG NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE / CITRIC ACID REMARK 280 BUFFER, PH 7.6, 20% PEG3000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 18.21250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.30700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.14050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.30700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.21250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.14050 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ3 LYS B 19 O HOH B 202 1.58 REMARK 500 HG1 THR B 111 O HOH B 206 1.59 REMARK 500 NE2 GLN B 94 O HOH B 201 1.91 REMARK 500 O HOH A 253 O HOH A 306 1.97 REMARK 500 OE2 GLU A 43 O HOH A 201 2.04 REMARK 500 OE2 GLU B 15 O HOH B 202 2.07 REMARK 500 NZ LYS B 3 O HOH B 203 2.15 REMARK 500 O HOH A 270 O HOH B 289 2.15 REMARK 500 NZ LYS B 19 O HOH B 202 2.17 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 92 -93.14 -133.00 REMARK 500 ASN A 132 63.63 -153.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 325 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 326 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A 327 DISTANCE = 6.22 ANGSTROMS DBREF 5OJW A 1 152 UNP P52490 UBC13_YEAST 1 152 DBREF 5OJW B 1 137 UNP P53152 MMS2_YEAST 1 137 SEQRES 1 A 152 MET ALA SER LEU PRO LYS ARG ILE ILE LYS GLU THR GLU SEQRES 2 A 152 LYS LEU VAL SER ASP PRO VAL PRO GLY ILE THR ALA GLU SEQRES 3 A 152 PRO HIS ASP ASP ASN LEU ARG TYR PHE GLN VAL THR ILE SEQRES 4 A 152 GLU GLY PRO GLU GLN SER PRO TYR GLU ASP GLY ILE PHE SEQRES 5 A 152 GLU LEU GLU LEU TYR LEU PRO ASP ASP TYR PRO MET GLU SEQRES 6 A 152 ALA PRO LYS VAL ARG PHE LEU THR LYS ILE TYR HIS PRO SEQRES 7 A 152 ASN ILE ASP ARG LEU GLY ARG ILE CYS LEU ASP VAL LEU SEQRES 8 A 152 LYS THR ASN TRP SER PRO ALA LEU GLN ILE ARG THR VAL SEQRES 9 A 152 LEU LEU SER ILE GLN ALA LEU LEU ALA SER PRO ASN PRO SEQRES 10 A 152 ASN ASP PRO LEU ALA ASN ASP VAL ALA GLU ASP TRP ILE SEQRES 11 A 152 LYS ASN GLU GLN GLY ALA LYS ALA LYS ALA ARG GLU TRP SEQRES 12 A 152 THR LYS LEU TYR ALA LYS LYS LYS PRO SEQRES 1 B 137 MET SER LYS VAL PRO ARG ASN PHE ARG LEU LEU GLU GLU SEQRES 2 B 137 LEU GLU LYS GLY GLU LYS GLY PHE GLY PRO GLU SER CYS SEQRES 3 B 137 SER TYR GLY LEU ALA ASP SER ASP ASP ILE THR MET THR SEQRES 4 B 137 LYS TRP ASN GLY THR ILE LEU GLY PRO PRO HIS SER ASN SEQRES 5 B 137 HIS GLU ASN ARG ILE TYR SER LEU SER ILE ASP CYS GLY SEQRES 6 B 137 PRO ASN TYR PRO ASP SER PRO PRO LYS VAL THR PHE ILE SEQRES 7 B 137 SER LYS ILE ASN LEU PRO CYS VAL ASN PRO THR THR GLY SEQRES 8 B 137 GLU VAL GLN THR ASP PHE HIS THR LEU ARG ASP TRP LYS SEQRES 9 B 137 ARG ALA TYR THR MET GLU THR LEU LEU LEU ASP LEU ARG SEQRES 10 B 137 LYS GLU MET ALA THR PRO ALA ASN LYS LYS LEU ARG GLN SEQRES 11 B 137 PRO LYS GLU GLY GLU THR PHE FORMUL 3 HOH *246(H2 O) HELIX 1 AA1 PRO A 5 ASP A 18 1 14 HELIX 2 AA2 LEU A 88 LYS A 92 5 5 HELIX 3 AA3 GLN A 100 SER A 114 1 15 HELIX 4 AA4 ALA A 122 ASN A 132 1 11 HELIX 5 AA5 ASN A 132 ALA A 148 1 17 HELIX 6 AA6 PRO B 5 LYS B 19 1 15 HELIX 7 AA7 PHE B 97 ASP B 102 1 6 HELIX 8 AA8 THR B 108 ALA B 121 1 14 HELIX 9 AA9 THR B 122 LYS B 127 1 6 SHEET 1 AA1 4 ILE A 23 HIS A 28 0 SHEET 2 AA1 4 ASN A 31 GLU A 40 -1 O TYR A 34 N HIS A 28 SHEET 3 AA1 4 GLY A 50 TYR A 57 -1 O LEU A 56 N PHE A 35 SHEET 4 AA1 4 LYS A 68 PHE A 71 -1 O LYS A 68 N TYR A 57 SHEET 1 AA2 4 ILE A 23 HIS A 28 0 SHEET 2 AA2 4 ASN A 31 GLU A 40 -1 O TYR A 34 N HIS A 28 SHEET 3 AA2 4 GLY A 50 TYR A 57 -1 O LEU A 56 N PHE A 35 SHEET 4 AA2 4 LYS A 149 LYS A 150 -1 O LYS A 149 N ILE A 51 SHEET 1 AA3 4 CYS B 26 LEU B 30 0 SHEET 2 AA3 4 LYS B 40 LEU B 46 -1 O ASN B 42 N GLY B 29 SHEET 3 AA3 4 ILE B 57 ASP B 63 -1 O ILE B 62 N TRP B 41 SHEET 4 AA3 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 13.97 CISPEP 2 TYR B 68 PRO B 69 0 0.96 CRYST1 36.425 66.281 126.614 90.00 90.00 90.00 P 21 21 21 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 0.027454 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015087 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007898 0.00000