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- PDB-1wzw: Crystal Structure of UbcH8 -

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Basic information

Entry
Database: PDB / ID: 1wzw
TitleCrystal Structure of UbcH8
ComponentsUbiquitin-conjugating enzyme E2 L6
KeywordsLIGASE / UBIQUITIN / UBIQUITIN CONJUGATING ENZYME / E2
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / E2 ubiquitin-conjugating enzyme / RSV-host interactions / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / ubiquitin binding / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta ...ISG15 transferase activity / ISG15-protein conjugation / E2 ubiquitin-conjugating enzyme / RSV-host interactions / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / ubiquitin binding / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein modification process / PKR-mediated signaling / ISG15 antiviral mechanism / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / Amyloid fiber formation / innate immune response / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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/ISG15-conjugating enzyme E2 L6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMizushima, T. / Suzuki, M. / Teshima, N. / Yamane, T. / Murata, S. / Tanaka, K.
CitationJournal: To be Published
Title: Crystal Structure of UbcH8
Authors: Mizushima, T. / Suzuki, M. / Teshima, N. / Yamane, T. / Murata, S. / Tanaka, K.
History
DepositionMar 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 L6


Theoretical massNumber of molelcules
Total (without water)17,9421
Polymers17,9421
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.932, 33.424, 50.432
Angle α, β, γ (deg.)90.00, 108.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-165-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 L6 / Ubiquitin-Conjugating Enzyme UbcH8 / Ubiquitin-protein ligase L6 / Ubiquitin carrier protein L6 / ...Ubiquitin-Conjugating Enzyme UbcH8 / Ubiquitin-protein ligase L6 / Ubiquitin carrier protein L6 / UbcH8 / Retinoic acid induced gene B protein / RIG-B


Mass: 17941.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIPL) / References: UniProt: O14933, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 6025 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.32 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.123 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.446 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.756 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27362 268 4.6 %RANDOM
Rwork0.19998 ---
all0.20324 ---
obs0.20324 5577 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.499 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å2-0.35 Å2
2--2.96 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 0 32 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221262
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9941721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80724.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64815219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.386159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02968
X-RAY DIFFRACTIONr_nbd_refined0.2130.2613
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.23
X-RAY DIFFRACTIONr_mcbond_it0.8691.5784
X-RAY DIFFRACTIONr_mcangle_it1.52221260
X-RAY DIFFRACTIONr_scbond_it2.3633533
X-RAY DIFFRACTIONr_scangle_it4.0664.5461
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 22 -
Rwork0.259 336 -
obs--84.83 %

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