PDB Short entry for 6CYR HEADER LIGASE, TRANSFERASE 06-APR-18 6CYR TITLE CRYSTAL STRUCTURE OF THE UBE2A VARIANT Q93E 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; COMPND 8 MUTATION: 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, Q93E VARIANT, LIGASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.T.RANZANI,J.F.DE OLIVEIRA REVDAT 3 04-OCT-23 6CYR 1 REMARK REVDAT 2 19-DEC-18 6CYR 1 JRNL REVDAT 1 12-DEC-18 6CYR 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 484 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 45.1227 - 3.1727 1.00 3062 159 0.1738 0.2092 REMARK 3 2 3.1727 - 2.5184 1.00 2920 164 0.2546 0.3078 REMARK 3 3 2.5184 - 2.2000 1.00 2860 161 0.2815 0.3652 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.55 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): 9.5589 -3.7203 19.9570 REMARK 3 T TENSOR REMARK 3 T11: 0.3247 T22: 0.3215 REMARK 3 T33: 0.3134 T12: 0.0254 REMARK 3 T13: -0.0235 T23: -0.0163 REMARK 3 L TENSOR REMARK 3 L11: 4.6188 L22: 1.7317 REMARK 3 L33: 4.5916 L12: -1.0215 REMARK 3 L13: -2.6425 L23: 0.9007 REMARK 3 S TENSOR REMARK 3 S11: 0.0625 S12: -0.0292 S13: 0.2582 REMARK 3 S21: -0.0276 S22: -0.0405 S23: -0.0435 REMARK 3 S31: -0.2634 S32: 0.0548 S33: -0.0245 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 6CYR 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_1000233740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-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) : 1.45868 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 : 9371 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.113 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.28900 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: 6CYO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 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 18.75550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.29500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.20950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.29500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.75550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.20950 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 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 ASP A 19 58.15 -146.38 REMARK 500 ASP A 50 -6.89 73.39 REMARK 500 ARG A 95 44.98 -109.88 REMARK 500 ASN A 133 81.99 -154.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6CYO RELATED DB: PDB DBREF 6CYR A 1 152 UNP P49459 UBE2A_HUMAN 1 152 SEQADV 6CYR GLY A -2 UNP P49459 EXPRESSION TAG SEQADV 6CYR SER A -1 UNP P49459 EXPRESSION TAG SEQADV 6CYR HIS A 0 UNP P49459 EXPRESSION TAG SEQADV 6CYR GLU A 93 UNP P49459 GLN 93 ENGINEERED MUTATION 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 GLU 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 *26(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 SER A 148 1 16 SHEET 1 AA1 4 VAL A 24 PRO A 28 0 SHEET 2 AA1 4 VAL A 35 PHE A 41 -1 O VAL A 39 N SER A 25 SHEET 3 AA1 4 THR A 52 GLU A 58 -1 O LEU A 55 N ALA A 38 SHEET 4 AA1 4 THR A 69 PHE A 72 -1 O THR A 69 N GLU A 58 SSBOND 1 CYS A 88 CYS A 152 1555 3655 2.03 CISPEP 1 TYR A 63 PRO A 64 0 5.86 CRYST1 37.511 52.419 88.590 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 0.026659 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011288 0.00000