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- PDB-3l1x: Crystal Structure of U-box Domain of Human E4B Ubiquitin Ligase -

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Basic information

Entry
Database: PDB / ID: 3l1x
TitleCrystal Structure of U-box Domain of Human E4B Ubiquitin Ligase
ComponentsUbiquitin conjugation factor E4 B
KeywordsLIGASE / E3 UBIQUITIN LIGASE / E4 UBIQUITIN LIGASE / U-BOX DOMAIN / Ubl conjugation pathway
Function / homology
Function and homology information


granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / : / response to UV / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding ...granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / : / response to UV / ubiquitin ligase complex / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding / nucleus / cytoplasm
Similarity search - Function
Ubiquitin conjugation factor E4 / Ubiquitin conjugation factor E4, core / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type ...Ubiquitin conjugation factor E4 / Ubiquitin conjugation factor E4, core / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin conjugation factor E4 B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBenirschke, R. / Thompson, J.R. / Mer, G.
CitationJournal: Structure / Year: 2010
Title: Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4.
Authors: Benirschke, R.C. / Thompson, J.R. / Nomine, Y. / Wasielewski, E. / Juranic, N. / Macura, S. / Hatakeyama, S. / Nakayama, K.I. / Botuyan, M.V. / Mer, G.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 conjugation factor E4 B


Theoretical massNumber of molelcules
Total (without water)11,5491
Polymers11,5491
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.395, 83.395, 83.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-6-

HOH

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Components

#1: Protein Ubiquitin conjugation factor E4 B / Ubiquitin fusion degradation protein 2 / Homozygously deleted in neuroblastoma 1


Mass: 11548.991 Da / Num. of mol.: 1 / Fragment: U box domain, residues 1208-1302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE4B, HDNB1, KIAA0684, UFD2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O95155
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2M TACSIMATE, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→24.074 Å / Num. obs: 3328 / % possible obs: 99.92 % / Redundancy: 37 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 46.18
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 36.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 7.29 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EZJ

2ezj
PDB Unreleased entry


Resolution: 2.6→24.07 Å / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 304 9.13 %RANDOM
Rwork0.1853 ---
obs0.1913 3328 98.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.115 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 42.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 0 33 639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002639
X-RAY DIFFRACTIONf_angle_d0.588870
X-RAY DIFFRACTIONf_dihedral_angle_d16.493266
X-RAY DIFFRACTIONf_chiral_restr0.04198
X-RAY DIFFRACTIONf_plane_restr0.003116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-3.27890.34721480.2361465X-RAY DIFFRACTION99
3.2789-24.07510.2131560.16281559X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -4.2179 Å / Origin y: 19.6556 Å / Origin z: 31.0241 Å
111213212223313233
T0.1907 Å2-0.0098 Å2-0.0491 Å2-0.1837 Å20.0429 Å2--0.1466 Å2
L1.0128 °2-0.3882 °20.2476 °2-0.4682 °2-0.4129 °2--0.3277 °2
S-0.08 Å °0.2382 Å °0.1078 Å °-0.1426 Å °0.071 Å °0.0123 Å °0.0787 Å °-0.0141 Å °-0 Å °
Refinement TLS groupSelection details: chain A

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