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 <I/SIGMA(I)> 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 <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: 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
(ATOM LINES ARE NOT SHOWN.)
END
