HEADER TRANSFERASE 27-OCT-15 5EGG TITLE CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME UBCH5C COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-CONJUGATING ENZYME UBCH5C,(E3-INDEPENDENT) E2 COMPND 5 UBIQUITIN-CONJUGATING ENZYME D3,E2 UBIQUITIN-CONJUGATING ENZYME D3, COMPND 6 UBIQUITIN CARRIER PROTEIN D3,UBIQUITIN-CONJUGATING ENZYME E2(17)KB 3, COMPND 7 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3,UBIQUITIN-PROTEIN LIGASE D3; COMPND 8 EC: 2.3.2.23,2.3.2.24; COMPND 9 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: UBE2D3, UBC5C, UBCH5C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS BIQUITIN-CONJUGATING ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHU,H.LI,F.WU,J.ZHU REVDAT 3 08-NOV-23 5EGG 1 JRNL REMARK REVDAT 2 26-JUL-17 5EGG 1 JRNL REMARK REVDAT 1 02-NOV-16 5EGG 0 JRNL AUTH F.WU,J.ZHU,H.LI,L.ZHU JRNL TITL STRUCTURAL ANALYSIS OF RECOMBINANT HUMAN JRNL TITL 2 UBIQUITIN-CONJUGATING ENZYME UBCH5C JRNL REF ACTA PHARM SIN B V. 7 390 2017 JRNL REFN ISSN 2211-3835 JRNL PMID 28540177 JRNL DOI 10.1016/J.APSB.2016.12.008 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.810 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 750 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 30.4288 - 3.0088 0.98 2938 128 0.1916 0.2271 REMARK 3 2 3.0088 - 2.3885 1.00 2832 134 0.2142 0.2617 REMARK 3 3 2.3885 - 2.0866 1.00 2804 161 0.2091 0.2562 REMARK 3 4 2.0866 - 1.8959 1.00 2735 165 0.2255 0.2781 REMARK 3 5 1.8959 - 1.7600 1.00 2738 162 0.2385 0.3134 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.870 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 1213 REMARK 3 ANGLE : 1.316 1654 REMARK 3 CHIRALITY : 0.054 178 REMARK 3 PLANARITY : 0.008 216 REMARK 3 DIHEDRAL : 12.903 457 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): -12.5398 -20.7440 14.7688 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.1773 REMARK 3 T33: 0.1251 T12: -0.0379 REMARK 3 T13: 0.0204 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 0.8544 L22: 4.6128 REMARK 3 L33: 0.8007 L12: 1.2660 REMARK 3 L13: 0.0616 L23: -1.1412 REMARK 3 S TENSOR REMARK 3 S11: -0.2710 S12: 0.2088 S13: -0.0199 REMARK 3 S21: -0.3930 S22: 0.2908 S23: -0.1912 REMARK 3 S31: 0.0489 S32: -0.1435 S33: -0.0277 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 5EGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000214797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-13 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97852 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14797 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 30.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 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: AUTOMAR REMARK 200 STARTING MODEL: 1X23 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% V/V TACSIMATE PH 4.0, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6, 16% W/V POLYETHYLENE GLYCOL 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.37000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.14000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.37000 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 MET A -8 REMARK 465 GLY A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 4 CG CD CE NZ REMARK 480 LYS A 63 CD CE NZ REMARK 480 ARG A 90 NE CZ NH1 NH2 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 OXT MET A 147 O HOH A 201 1.96 REMARK 500 O HOH A 251 O HOH A 258 2.00 REMARK 500 O HOH A 242 O HOH A 259 2.03 REMARK 500 O HOH A 250 O HOH A 258 2.10 REMARK 500 O HOH A 250 O HOH A 251 2.14 REMARK 500 O HOH A 209 O HOH A 266 2.18 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 GLN A 20 -55.54 -123.92 REMARK 500 ARG A 90 -104.93 -131.32 REMARK 500 ASN A 114 78.52 -115.82 REMARK 500 ASP A 130 84.26 -151.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 5EGG A 1 147 UNP P61077 UB2D3_HUMAN 1 147 SEQADV 5EGG MET A -8 UNP P61077 EXPRESSION TAG SEQADV 5EGG GLY A -7 UNP P61077 EXPRESSION TAG SEQADV 5EGG HIS A -6 UNP P61077 EXPRESSION TAG SEQADV 5EGG HIS A -5 UNP P61077 EXPRESSION TAG SEQADV 5EGG HIS A -4 UNP P61077 EXPRESSION TAG SEQADV 5EGG HIS A -3 UNP P61077 EXPRESSION TAG SEQADV 5EGG HIS A -2 UNP P61077 EXPRESSION TAG SEQADV 5EGG HIS A -1 UNP P61077 EXPRESSION TAG SEQADV 5EGG GLY A 0 UNP P61077 EXPRESSION TAG SEQRES 1 A 156 MET GLY HIS HIS HIS HIS HIS HIS GLY MET ALA LEU LYS SEQRES 2 A 156 ARG ILE ASN LYS GLU LEU SER ASP LEU ALA ARG ASP PRO SEQRES 3 A 156 PRO ALA GLN CYS SER ALA GLY PRO VAL GLY ASP ASP MET SEQRES 4 A 156 PHE HIS TRP GLN ALA THR ILE MET GLY PRO ASN ASP SER SEQRES 5 A 156 PRO TYR GLN GLY GLY VAL PHE PHE LEU THR ILE HIS PHE SEQRES 6 A 156 PRO THR ASP TYR PRO PHE LYS PRO PRO LYS VAL ALA PHE SEQRES 7 A 156 THR THR ARG ILE TYR HIS PRO ASN ILE ASN SER ASN GLY SEQRES 8 A 156 SER ILE CYS LEU ASP ILE LEU ARG SER GLN TRP SER PRO SEQRES 9 A 156 ALA LEU THR ILE SER LYS VAL LEU LEU SER ILE CYS SER SEQRES 10 A 156 LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO LEU VAL PRO SEQRES 11 A 156 GLU ILE ALA ARG ILE TYR LYS THR ASP ARG ASP LYS TYR SEQRES 12 A 156 ASN ARG ILE SER ARG GLU TRP THR GLN LYS TYR ALA MET FORMUL 2 HOH *67(H2 O) HELIX 1 AA1 GLY A 0 ASP A 16 1 17 HELIX 2 AA2 LEU A 86 ARG A 90 5 5 HELIX 3 AA3 THR A 98 ASP A 112 1 15 HELIX 4 AA4 VAL A 120 ASP A 130 1 11 HELIX 5 AA5 ASP A 130 ALA A 146 1 17 SHEET 1 AA1 4 SER A 22 PRO A 25 0 SHEET 2 AA1 4 HIS A 32 MET A 38 -1 O THR A 36 N SER A 22 SHEET 3 AA1 4 VAL A 49 HIS A 55 -1 O ILE A 54 N TRP A 33 SHEET 4 AA1 4 LYS A 66 PHE A 69 -1 O ALA A 68 N THR A 53 CISPEP 1 TYR A 60 PRO A 61 0 10.30 CRYST1 28.170 66.280 76.740 90.00 90.00 90.00 P 2 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 0.035499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013031 0.00000