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- PDB-8hm1: crystal structure of human ubiquitin-like protein from Bacteroide... -

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Basic information

Entry
Database: PDB / ID: 8hm1
Titlecrystal structure of human ubiquitin-like protein from Bacteroides fragilis
ComponentsPutative ubiquitin
KeywordsCELL CYCLE / ubiquitin-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: 1.29 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ubiquitin
B: Putative ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,31511
Polymers17,7562
Non-polymers5599
Water4,306239
1
A: Putative ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3138
Polymers8,8781
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0023
Polymers8,8781
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.380, 38.380, 190.860
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

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Components

#1: Protein Putative ubiquitin


Mass: 8878.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: ubb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5L8M7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium citrate pH 3.0, 3.4 M cesium chloride

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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: 1.29→32.86 Å / Num. obs: 36628 / % possible obs: 98.07 % / Redundancy: 20 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.1
Reflection shellResolution: 1.29→1.336 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3124 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
XDS1.19.2_4158data reduction
PHENIX1.19.2_4158refinement
Cootmodel building
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.29→32.86 Å / SU ML: 0.1928 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 1876 5.12 %
Rwork0.2492 34752 -
obs0.25 36628 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.16 Å2
Refinement stepCycle: LAST / Resolution: 1.29→32.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 36 239 1515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01851285
X-RAY DIFFRACTIONf_angle_d1.93591714
X-RAY DIFFRACTIONf_chiral_restr0.1085192
X-RAY DIFFRACTIONf_plane_restr0.0116218
X-RAY DIFFRACTIONf_dihedral_angle_d14.5194497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.36351180.33762260X-RAY DIFFRACTION84.39
1.32-1.360.33421440.3162439X-RAY DIFFRACTION92.61
1.36-1.410.30051280.28892599X-RAY DIFFRACTION97.81
1.41-1.460.29691410.27442674X-RAY DIFFRACTION100
1.46-1.520.31041600.2682665X-RAY DIFFRACTION100
1.52-1.590.28381520.2582676X-RAY DIFFRACTION100
1.59-1.670.24011370.24912713X-RAY DIFFRACTION100
1.67-1.770.26351510.24322677X-RAY DIFFRACTION100
1.77-1.910.30121430.24672729X-RAY DIFFRACTION100
1.91-2.10.2511540.2372730X-RAY DIFFRACTION100
2.1-2.410.22371250.23432789X-RAY DIFFRACTION99.97
2.41-3.030.2331660.24282790X-RAY DIFFRACTION100
3.03-32.860.27551570.24923011X-RAY DIFFRACTION99.78

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