PDB Short entry for 6CYO HEADER LIGASE, TRANSFERASE 06-APR-18 6CYO TITLE CRYSTAL STRUCTURE OF HUMAN UBE2A (RAD6A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME A,RAD6 HOMOLOG A,HHR6A, COMPND 5 UBIQUITIN CARRIER PROTEIN A,UBIQUITIN-PROTEIN LIGASE A; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2A, RAD6A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA II(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS UBIQUITIN-CONJUNGATING ENZYME E2 A, LIGASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.T.RANZANI,J.F.DE OLIVEIRA REVDAT 3 04-OCT-23 6CYO 1 REMARK REVDAT 2 19-DEC-18 6CYO 1 JRNL REVDAT 1 12-DEC-18 6CYO 0 JRNL AUTH J.F.DE OLIVEIRA,P.F.V.DO PRADO,S.S.DA COSTA,M.L.SFORCA, JRNL AUTH 2 C.CANATELI,A.T.RANZANI,M.MASCHIETTO,P.S.L.DE OLIVEIRA, JRNL AUTH 3 P.A.OTTO,R.E.KLEVIT,A.C.V.KREPISCHI,C.ROSENBERG, JRNL AUTH 4 K.G.FRANCHINI JRNL TITL MECHANISTIC INSIGHTS REVEALED BY A UBE2A MUTATION LINKED TO JRNL TITL 2 INTELLECTUAL DISABILITY. JRNL REF NAT. CHEM. BIOL. V. 15 62 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 30531907 JRNL DOI 10.1038/S41589-018-0177-2 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 15115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 728 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 28.6606 - 3.1624 1.00 3011 170 0.1760 0.1755 REMARK 3 2 3.1624 - 2.5105 1.00 2922 132 0.2396 0.2656 REMARK 3 3 2.5105 - 2.1933 1.00 2871 127 0.2348 0.2853 REMARK 3 4 2.1933 - 1.9928 1.00 2837 166 0.2316 0.2717 REMARK 3 5 1.9928 - 1.8500 0.97 2746 133 0.2728 0.2950 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.42 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 9.4922 -3.8424 19.9134 REMARK 3 T TENSOR REMARK 3 T11: 0.2290 T22: 0.2039 REMARK 3 T33: 0.3045 T12: 0.0010 REMARK 3 T13: -0.0217 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 3.3205 L22: 1.7479 REMARK 3 L33: 5.0036 L12: -0.9972 REMARK 3 L13: -2.3283 L23: 1.0833 REMARK 3 S TENSOR REMARK 3 S11: 0.1156 S12: -0.0589 S13: 0.2963 REMARK 3 S21: 0.0465 S22: -0.0276 S23: -0.0071 REMARK 3 S31: -0.2699 S32: 0.0801 S33: -0.0876 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 6CYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-16 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 : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.45863 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 44.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 1.69200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2YB6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM DI-SODIUM SUCCINATE PH 7.0 AND REMARK 280 12-14% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 18.74850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.33150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.67500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.33150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.74850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.67500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 CYS A 152 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 MET A 1 13.45 -143.57 REMARK 500 ASP A 50 -9.32 80.50 REMARK 500 ASN A 133 77.56 -160.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 6CYO A 1 152 UNP P49459 UBE2A_HUMAN 1 152 SEQADV 6CYO GLY A -2 UNP P49459 EXPRESSION TAG SEQADV 6CYO SER A -1 UNP P49459 EXPRESSION TAG SEQADV 6CYO HIS A 0 UNP P49459 EXPRESSION TAG SEQRES 1 A 155 GLY SER HIS MET SER THR PRO ALA ARG ARG ARG LEU MET SEQRES 2 A 155 ARG ASP PHE LYS ARG LEU GLN GLU ASP PRO PRO ALA GLY SEQRES 3 A 155 VAL SER GLY ALA PRO SER GLU ASN ASN ILE MET VAL TRP SEQRES 4 A 155 ASN ALA VAL ILE PHE GLY PRO GLU GLY THR PRO PHE GLU SEQRES 5 A 155 ASP GLY THR PHE LYS LEU THR ILE GLU PHE THR GLU GLU SEQRES 6 A 155 TYR PRO ASN LYS PRO PRO THR VAL ARG PHE VAL SER LYS SEQRES 7 A 155 MET PHE HIS PRO ASN VAL TYR ALA ASP GLY SER ILE CYS SEQRES 8 A 155 LEU ASP ILE LEU GLN ASN ARG TRP SER PRO THR TYR ASP SEQRES 9 A 155 VAL SER SER ILE LEU THR SER ILE GLN SER LEU LEU ASP SEQRES 10 A 155 GLU PRO ASN PRO ASN SER PRO ALA ASN SER GLN ALA ALA SEQRES 11 A 155 GLN LEU TYR GLN GLU ASN LYS ARG GLU TYR GLU LYS ARG SEQRES 12 A 155 VAL SER ALA ILE VAL GLU GLN SER TRP ARG ASP CYS FORMUL 2 HOH *72(H2 O) HELIX 1 AA1 THR A 3 ASP A 19 1 17 HELIX 2 AA2 LEU A 89 ASN A 94 1 6 HELIX 3 AA3 ASP A 101 GLU A 115 1 15 HELIX 4 AA4 ASN A 123 ASN A 133 1 11 HELIX 5 AA5 ASN A 133 TRP A 149 1 17 SHEET 1 AA1 4 VAL A 24 PRO A 28 0 SHEET 2 AA1 4 VAL A 35 PHE A 41 -1 O ASN A 37 N ALA A 27 SHEET 3 AA1 4 THR A 52 GLU A 58 -1 O ILE A 57 N TRP A 36 SHEET 4 AA1 4 THR A 69 PHE A 72 -1 O THR A 69 N GLU A 58 CISPEP 1 TYR A 63 PRO A 64 0 9.00 CRYST1 37.497 51.350 88.663 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 0.026669 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011279 0.00000