HEADER TRANSFERASE 12-MAR-24 9EN5 TITLE CRYSTAL STRUCTURE OF YEAST E2 UBIQUITIN-CONJUGATING ENZYME UBC6 UBC TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME 6,UBIQUITIN CARRIER PROTEIN COMPND 5 UBC6,UBIQUITIN-PROTEIN LIGASE UBC6; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_TAXID: 559292; SOURCE 4 GENE: UBC6, DOA2, YER100W; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, ENDOPLASMIC RETICULUM, NON-CANONICAL UBIQUITINATION, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SWARNKAR,A.STEIN REVDAT 3 25-DEC-24 9EN5 1 JRNL REVDAT 2 27-NOV-24 9EN5 1 JRNL REVDAT 1 20-NOV-24 9EN5 0 JRNL AUTH A.SWARNKAR,F.LEIDNER,A.K.ROUT,S.AINATZI,C.C.SCHMIDT, JRNL AUTH 2 S.BECKER,H.URLAUB,C.GRIESINGER,H.GRUBMULLER,A.STEIN JRNL TITL DETERMINANTS OF CHEMOSELECTIVITY IN UBIQUITINATION BY THE J2 JRNL TITL 2 FAMILY OF UBIQUITIN-CONJUGATING ENZYMES. JRNL REF EMBO J. V. 43 6705 2024 JRNL REFN ESSN 1460-2075 JRNL PMID 39533056 JRNL DOI 10.1038/S44318-024-00301-3 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 40913 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2041 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 44.8000 - 3.2800 1.00 2952 153 0.1585 0.1762 REMARK 3 2 3.2800 - 2.6000 1.00 2808 148 0.1553 0.1696 REMARK 3 3 2.6000 - 2.2800 1.00 2794 146 0.1482 0.1685 REMARK 3 4 2.2800 - 2.0700 1.00 2769 145 0.1353 0.1712 REMARK 3 5 2.0700 - 1.9200 1.00 2734 144 0.1467 0.1650 REMARK 3 6 1.9200 - 1.8100 1.00 2761 145 0.1383 0.1833 REMARK 3 7 1.8100 - 1.7200 1.00 2748 143 0.1374 0.2044 REMARK 3 8 1.7200 - 1.6400 1.00 2711 143 0.1605 0.2129 REMARK 3 9 1.6400 - 1.5800 1.00 2715 142 0.1769 0.2208 REMARK 3 10 1.5800 - 1.5200 1.00 2715 144 0.1603 0.1977 REMARK 3 11 1.5200 - 1.4800 1.00 2718 143 0.1640 0.2044 REMARK 3 12 1.4800 - 1.4300 0.94 2572 135 0.1902 0.2649 REMARK 3 13 1.4300 - 1.4000 0.82 2248 119 0.2854 0.3315 REMARK 3 14 1.4000 - 1.3600 0.72 1930 102 0.4300 0.5120 REMARK 3 15 1.3600 - 1.3300 0.63 1697 89 0.6616 0.6000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.192 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.779 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.31 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 : 0.012 1430 REMARK 3 ANGLE : 1.239 1952 REMARK 3 CHIRALITY : 0.104 212 REMARK 3 PLANARITY : 0.012 252 REMARK 3 DIHEDRAL : 5.604 191 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 9EN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292137117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 44.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.03871 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.39000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DI-AMMONIUM HYDROGEN REMARK 280 CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 22.01000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.10550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.69200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.10550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.01000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.69200 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: 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 LEU A 170 REMARK 465 ASP A 171 REMARK 465 GLU A 172 REMARK 465 LEU A 173 REMARK 465 PRO A 174 REMARK 465 GLU A 175 REMARK 465 THR A 176 REMARK 465 GLY A 177 REMARK 465 GLY A 178 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 ASN A 33 97.47 -161.72 REMARK 500 ASN A 77 -22.77 -145.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 9EN5 A 1 172 UNP P33296 UBC6_YEAST 1 172 SEQADV 9EN5 LEU A 173 UNP P33296 EXPRESSION TAG SEQADV 9EN5 PRO A 174 UNP P33296 EXPRESSION TAG SEQADV 9EN5 GLU A 175 UNP P33296 EXPRESSION TAG SEQADV 9EN5 THR A 176 UNP P33296 EXPRESSION TAG SEQADV 9EN5 GLY A 177 UNP P33296 EXPRESSION TAG SEQADV 9EN5 GLY A 178 UNP P33296 EXPRESSION TAG SEQRES 1 A 178 MET ALA THR LYS GLN ALA HIS LYS ARG LEU THR LYS GLU SEQRES 2 A 178 TYR LYS LEU MET VAL GLU ASN PRO PRO PRO TYR ILE LEU SEQRES 3 A 178 ALA ARG PRO ASN GLU ASP ASN ILE LEU GLU TRP HIS TYR SEQRES 4 A 178 ILE ILE THR GLY PRO ALA ASP THR PRO TYR LYS GLY GLY SEQRES 5 A 178 GLN TYR HIS GLY THR LEU THR PHE PRO SER ASP TYR PRO SEQRES 6 A 178 TYR LYS PRO PRO ALA ILE ARG MET ILE THR PRO ASN GLY SEQRES 7 A 178 ARG PHE LYS PRO ASN THR ARG LEU CYS LEU SER MET SER SEQRES 8 A 178 ASP TYR HIS PRO ASP THR TRP ASN PRO GLY TRP SER VAL SEQRES 9 A 178 SER THR ILE LEU ASN GLY LEU LEU SER PHE MET THR SER SEQRES 10 A 178 ASP GLU ALA THR THR GLY SER ILE THR THR SER ASP HIS SEQRES 11 A 178 GLN LYS LYS THR LEU ALA ARG ASN SER ILE SER TYR ASN SEQRES 12 A 178 THR PHE GLN ASN VAL ARG PHE LYS LEU ILE PHE PRO GLU SEQRES 13 A 178 VAL VAL GLN GLU ASN VAL GLU THR LEU GLU LYS ARG LYS SEQRES 14 A 178 LEU ASP GLU LEU PRO GLU THR GLY GLY FORMUL 2 HOH *263(H2 O) HELIX 1 AA1 THR A 3 ASN A 20 1 18 HELIX 2 AA2 HIS A 94 TRP A 98 5 5 HELIX 3 AA3 SER A 103 SER A 117 1 15 HELIX 4 AA4 SER A 128 GLN A 146 1 19 HELIX 5 AA5 ASN A 147 PHE A 154 1 8 HELIX 6 AA6 PHE A 154 LYS A 169 1 16 SHEET 1 AA1 4 ILE A 25 ASN A 30 0 SHEET 2 AA1 4 ASN A 33 THR A 42 -1 O ILE A 40 N LEU A 26 SHEET 3 AA1 4 GLN A 53 THR A 59 -1 O TYR A 54 N ILE A 41 SHEET 4 AA1 4 ALA A 70 MET A 73 -1 O ALA A 70 N THR A 59 CISPEP 1 TYR A 64 PRO A 65 0 13.54 CRYST1 44.020 55.384 76.211 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 0.022717 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013121 0.00000