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- PDB-5x3p: Crystal structure of the UBX domain of human UBXD7 -

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Basic information

Entry
Database: PDB / ID: 5x3p
TitleCrystal structure of the UBX domain of human UBXD7
ComponentsUBX domain-containing protein 7
KeywordsPROTEIN BINDING / UBXD7 / p97
Function / homology
Function and homology information


VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin binding / KEAP1-NFE2L2 pathway / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
UBX domain-containing protein 2/7 / UAS / : / UAS / Thioredoxin-like / : / UBA-like domain / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain ...UBX domain-containing protein 2/7 / UAS / : / UAS / Thioredoxin-like / : / UBA-like domain / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UBX domain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å
AuthorsJiang, T. / Li, Z. / Wang, Y. / Xu, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structures of the UBX domain of human UBXD7 and its complex with p97 ATPase
Authors: Li, Z.H. / Wang, Y. / Xu, M. / Jiang, T.
History
DepositionFeb 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBX domain-containing protein 7
B: UBX domain-containing protein 7
C: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)28,9013
Polymers28,9013
Non-polymers00
Water2,972165
1
A: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)9,6341
Polymers9,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)9,6341
Polymers9,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UBX domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)9,6341
Polymers9,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.067, 78.038, 44.963
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UBX domain-containing protein 7


Mass: 9633.721 Da / Num. of mol.: 3 / Fragment: UNP residues 410-489 / Mutation: L472M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBXN7, KIAA0794, UBXD7 / Production host: Escherichia coli (E. coli) / References: UniProt: O94888
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.1M Tris pH 8.8, 35% v/v Polyethylene glycol 400, 0.1M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→38.24 Å / Num. obs: 14643 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.048 / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: SAD / Resolution: 1.999→38.24 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2262 713 5.02 %
Rwork0.1743 --
obs0.1769 14202 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.999→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 0 165 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091985
X-RAY DIFFRACTIONf_angle_d1.1752672
X-RAY DIFFRACTIONf_dihedral_angle_d15.924794
X-RAY DIFFRACTIONf_chiral_restr0.079289
X-RAY DIFFRACTIONf_plane_restr0.006351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9989-2.15320.28661210.20062376X-RAY DIFFRACTION85
2.1532-2.36990.25441530.1922721X-RAY DIFFRACTION99
2.3699-2.71270.26531540.18982769X-RAY DIFFRACTION100
2.7127-3.41740.22171450.17912782X-RAY DIFFRACTION100
3.4174-38.24740.19181400.15572841X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.5605 Å / Origin y: 75.6638 Å / Origin z: 7.0928 Å
111213212223313233
T0.1668 Å2-0.0193 Å20.0019 Å2-0.1552 Å20.0138 Å2--0.1513 Å2
L0.5547 °2-0.0659 °20.2046 °2-0.5534 °20.3829 °2--0.4934 °2
S0.0335 Å °-0.0493 Å °-0.1044 Å °0.1323 Å °0.0137 Å °-0.0806 Å °0.1675 Å °-0.0306 Å °-0.0073 Å °
Refinement TLS groupSelection details: all

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