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- PDB-4gpr: Crystal structure of EhUbc5, a ubiquitin conjugating enzyme from ... -

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Basic information

Entry
Database: PDB / ID: 4gpr
TitleCrystal structure of EhUbc5, a ubiquitin conjugating enzyme from Entamoeba histolytica
ComponentsUbiquitin-conjugating enzyme family protein
KeywordsLIGASE / E2 / Ubiquitin conjugating enzyme / ubiquitin conjugation / EhUba1 / EhRING1 / thiol esterification
Function / homology
Function and homology information


ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-dependent protein catabolic process / ATP binding / nucleus
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
: / Ubiquitin-conjugating enzyme family protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBosch, D.E. / Siderovski, D.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Determinants of Ubiquitin Conjugation in Entamoeba histolytica.
Authors: Bosch, D.E. / Siderovski, D.P.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1382
Polymers17,0791
Non-polymers591
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.973, 49.577, 63.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme family protein


Mass: 17079.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_070750, EHI_083560, EhUbc5 / Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / References: UniProt: C4M5T2
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: EhUbc5 at 8 mg/mL concentration in buffer containing 50 mM HEPES and 100 mM NaCl was mixed 1:1 and equilibrated against crystallization solution (100 mM Tris, 14% (w/v) polyvinylpyrrolidone ...Details: EhUbc5 at 8 mg/mL concentration in buffer containing 50 mM HEPES and 100 mM NaCl was mixed 1:1 and equilibrated against crystallization solution (100 mM Tris, 14% (w/v) polyvinylpyrrolidone K 15, and 0.5 mM cobalt (II) chloride), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 20139 / Num. obs: 19998 / % possible obs: 99.3 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 45.6
Reflection shellResolution: 1.6→1.61 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.8 / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CP4

2cp4


Resolution: 1.6→39.069 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 1998 10.02 %RANDOM
Rwork0.1706 ---
obs0.1737 19950 99.2 %-
all-20111 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 1 179 1375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141229
X-RAY DIFFRACTIONf_angle_d1.5041678
X-RAY DIFFRACTIONf_dihedral_angle_d13462
X-RAY DIFFRACTIONf_chiral_restr0.099183
X-RAY DIFFRACTIONf_plane_restr0.009222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64170.25951370.20571148X-RAY DIFFRACTION91
1.6417-1.6860.24841380.19661243X-RAY DIFFRACTION99
1.686-1.73570.21341450.18331264X-RAY DIFFRACTION100
1.7357-1.79170.22431300.19041282X-RAY DIFFRACTION100
1.7917-1.85570.25081380.18091263X-RAY DIFFRACTION100
1.8557-1.930.24531440.17921294X-RAY DIFFRACTION100
1.93-2.01780.21121470.17561273X-RAY DIFFRACTION100
2.0178-2.12420.21341400.16121284X-RAY DIFFRACTION100
2.1242-2.25730.19661440.16911286X-RAY DIFFRACTION100
2.2573-2.43160.2041420.16711288X-RAY DIFFRACTION100
2.4316-2.67620.2051470.18131291X-RAY DIFFRACTION100
2.6762-3.06330.21221430.17481308X-RAY DIFFRACTION100
3.0633-3.85890.19391460.16511330X-RAY DIFFRACTION100
3.8589-39.08080.16921570.15841398X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8784-0.8358-0.28971.24640.2640.93560.04960.0741-0.0365-0.0496-0.00970.0981-0.0369-0.1692-0.01460.06410.0139-0.05220.06130.00980.1185-14.29298.5744-3.7804
22.33330.11620.41583.39480.94980.3293-0.0125-0.8863-0.32830.5615-0.11480.18860.1123-0.0682-0.16580.12980.04460.00490.40360.04570.1806-7.68518.59086.3679
31.43990.3511-0.17551.20090.19961.3884-0.0870.02270.2710.04130.00180.4056-0.1347-0.1146-2.47160.03220.00560.04530.009-0.01240.0334-2.84899.33360.5974
41.48110.02380.55941.0512-0.26620.51040.02810.0774-0.0722-0.01420.05020.15590.0208-0.03280.80470.0856-0.01470.03560.0454-0.0160.0756-1.56442.57071.5732
52.168-0.0531-0.22691.8594-0.9530.51750.04190.29590.03720.0725-0.01330.0303-0.11270.169-0.02960.0595-0.01260.00690.0938-0.01260.06893.34122.664-0.4491
60.74790.70170.60810.80940.28011.85050.06560.1041-0.31060.0658-0.0512-0.17390.09980.4570.7617-0.03270.01440.0090.0305-0.01740.06678.3146-2.72186.0112
74.59012.49250.56063.4543-2.87854.90160.11650.2884-1.0854-0.44210.1409-0.33830.88530.17811.23220.15910.0089-0.0430.0847-0.0180.2023-2.6081-9.7312-2.897
82.38941.9212.26952.56081.09312.6898-0.0336-0.17680.0524-0.0230.01370.556-0.0187-0.27891.03220.0669-0.0098-0.02520.06150.02030.1686-10.0752-2.7719-2.3028
93.81180.53951.51661.26410.70526.14280.2546-0.3599-0.59790.2120.14510.05340.62460.04516.1670.0696-0.00740.0490.06130.01820.1765-1.9847-4.87419.3745
104.6885-0.03281.34542.50520.87447.41750.21330.1291-0.19350.1221-0.17560.32190.5498-0.0297-0.12190.14890.03960.0150.1263-0.05360.16799.0836-12.43976.5732
110.2362-0.15820.09590.45440.05760.078-0.02980.0701-0.29460.0806-0.0751-0.05160.43440.3425-1.61750.08720.3214-0.0393-0.04690.05150.120313.6125-12.023814.0864
121.5411-0.4231-0.20474.7959-2.02021.1280.0391-0.29850.10360.9284-0.2941-0.3838-0.51340.418-0.92610.1843-0.0434-0.03830.2108-0.01420.10689.87571.401518.545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:17)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:25)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 26:41)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 42:64)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 65:70)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 71:86)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 87:92)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 93:101)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 102:114)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 115:120)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 121:130)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 131:148)

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