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- PDB-8hm2: Crystal structure of human ubiquitin-like protein from bacteroide... -

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Basic information

Entry
Database: PDB / ID: 8hm2
TitleCrystal structure of human ubiquitin-like protein from bacteroides fragilis c terminal cysteine mutant
ComponentsPutative ubiquitin
KeywordsCELL CYCLE / ubiqutin like protein
Function / homology: / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Ubiquitin
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsTong, M. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122007 China
CitationJournal: Nat Microbiol / Year: 2024
Title: Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome.
Authors: Jiang, K. / Li, W. / Tong, M. / Xu, J. / Chen, Z. / Yang, Y. / Zang, Y. / Jiao, X. / Liu, C. / Lim, B. / Jiang, X. / Wang, J. / Wu, D. / Wang, M. / Liu, S.J. / Shao, F. / Gao, X.
History
DepositionDec 2, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ubiquitin
B: Putative ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,6562
Polymers17,6562
Non-polymers00
Water2,468137
1
A: Putative ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,8281
Polymers8,8281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,8281
Polymers8,8281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.537, 38.537, 177.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-143-

HOH

21A-153-

HOH

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Components

#1: Protein Putative ubiquitin


Mass: 8828.024 Da / Num. of mol.: 2 / Mutation: C70V, C76G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: ubb, BF9343_3779 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5L8M7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 2.8 / Details: 0.1M citric acid pH 2.8, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.34→29.07 Å / Num. obs: 30343 / % possible obs: 96.76 % / Redundancy: 20 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.994 / Net I/σ(I): 13.5
Reflection shellResolution: 1.34→1.388 Å / Num. unique obs: 2397 / CC1/2: 0.697

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
PHASERphasing
Cootmodel building
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.34→29.07 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 1475 4.86 %
Rwork0.2555 28868 -
obs0.2562 30343 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.45 Å2
Refinement stepCycle: LAST / Resolution: 1.34→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 137 1356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751248
X-RAY DIFFRACTIONf_angle_d1.06681687
X-RAY DIFFRACTIONf_chiral_restr0.0945192
X-RAY DIFFRACTIONf_plane_restr0.0071217
X-RAY DIFFRACTIONf_dihedral_angle_d13.4891487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.39011090.36062023X-RAY DIFFRACTION76.66
1.38-1.430.35621170.32322390X-RAY DIFFRACTION89.41
1.43-1.490.30631340.29972546X-RAY DIFFRACTION96.61
1.49-1.560.3231320.28342653X-RAY DIFFRACTION100
1.56-1.640.28441470.27512643X-RAY DIFFRACTION100
1.64-1.740.32411410.28492688X-RAY DIFFRACTION100
1.74-1.880.30081450.26362689X-RAY DIFFRACTION100
1.88-2.060.2991360.25552703X-RAY DIFFRACTION100
2.06-2.360.25711280.24092748X-RAY DIFFRACTION100
2.36-2.980.23831590.23832789X-RAY DIFFRACTION99.97
2.98-29.070.24381270.24172996X-RAY DIFFRACTION100

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