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- PDB-1zuo: Structure of Human Ubiquitin-Conjugating Enzyme (UBCi) Involved i... -

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Basic information

Entry
Database: PDB / ID: 1zuo
TitleStructure of Human Ubiquitin-Conjugating Enzyme (UBCi) Involved in Embryo Attachment and Implantation
ComponentsHypothetical protein LOC92912
KeywordsLIGASE / UBIQUITIN-CONJUGATING ENZYME / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ATP binding / nucleus / cytosol
Similarity search - Function
RWD domain / RWD domain / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like ...RWD domain / RWD domain / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Ubiquitin-conjugating enzyme E2 Q2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Cui, H. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Hypothetical protein LOC92912
B: Hypothetical protein LOC92912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7594
Polymers41,6032
Non-polymers1562
Water4,035224
1
A: Hypothetical protein LOC92912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8802
Polymers20,8021
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical protein LOC92912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8802
Polymers20,8021
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Hypothetical protein LOC92912
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)167,03816
Polymers166,4138
Non-polymers6258
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area15830 Å2
ΔGint-93 kcal/mol
Surface area48220 Å2
MethodPISA
4
A: Hypothetical protein LOC92912
hetero molecules

A: Hypothetical protein LOC92912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7594
Polymers41,6032
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area15690 Å2
MethodPISA
5
B: Hypothetical protein LOC92912
hetero molecules

B: Hypothetical protein LOC92912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7594
Polymers41,6032
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area1950 Å2
ΔGint-12 kcal/mol
Surface area14070 Å2
MethodPISA
6
B: Hypothetical protein LOC92912
hetero molecules

B: Hypothetical protein LOC92912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7594
Polymers41,6032
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area2310 Å2
ΔGint-15 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.442, 126.442, 104.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Hypothetical protein LOC92912


Mass: 20801.582 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 201-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LOC92912 / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVN8, ubiquitin-protein ligase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 298 K / pH: 5.8
Details: NACL, SODIUM CACODYLATE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 9, 2005 / Details: MIRRORS
RadiationMonochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 1.8→27.07 Å / Num. obs: 36041 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.631 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23239 1788 5 %RANDOM
Rwork0.1998 ---
obs0.20143 34253 91.43 %-
all-36041 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.471 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.28 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 8 224 2634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222461
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.973320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8155300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41224.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87915439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0121511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21086
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21722
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3920.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.25931542
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.24942418
X-RAY DIFFRACTIONr_scbond_it4.15951056
X-RAY DIFFRACTIONr_scangle_it5.9927902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 124 -
Rwork0.263 2583 -
obs--94.19 %

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