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- PDB-9ea5: Structure of Citrobacter BubCD D104A mutant -

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Basic information

Entry
Database: PDB / ID: 9ea5
TitleStructure of Citrobacter BubCD D104A mutant
ComponentsCitrobacter BubCD
KeywordsLIGASE / ubiquitin / E1 / DUB
Function / homologyACETIC ACID
Function and homology information
Biological speciesCitrobacter sp. RHBSTW-00271 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYe, Q. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144121 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: Mechanistic basis for protein conjugation in a diverged bacterial ubiquitination pathway.
Authors: Ye, Q. / Gong, M. / Cai, J. / Chambers, L.R. / Zhou, H. / Suhandynata, R.T. / Corbett, K.D.
History
DepositionNov 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 28, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrobacter BubCD
B: Citrobacter BubCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0597
Polymers101,8332
Non-polymers2265
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-49 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.868, 73.064, 98.399
Angle α, β, γ (deg.)90.000, 108.725, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Citrobacter BubCD


Mass: 50916.672 Da / Num. of mol.: 2 / Mutation: D104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RHBSTW-00271 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 44.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 8.5, 0.1 M sodium acetate, 10% Isopropanol, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→39.29 Å / Num. obs: 59172 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Net I/σ(I): 12
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.893 / Num. unique obs: 4350 / CC1/2: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.29 Å / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 2805 4.74 %
Rwork0.1722 56312 -
obs0.1738 59117 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.39 Å2
Refinement stepCycle: LAST / Resolution: 2→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 14 673 7449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266893
X-RAY DIFFRACTIONf_angle_d0.57139329
X-RAY DIFFRACTIONf_chiral_restr0.04371071
X-RAY DIFFRACTIONf_plane_restr0.00881212
X-RAY DIFFRACTIONf_dihedral_angle_d11.82382548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.25651380.2462761X-RAY DIFFRACTION97.97
2.03-2.070.26281200.20962830X-RAY DIFFRACTION98.17
2.07-2.110.27541460.21152717X-RAY DIFFRACTION96.76
2.11-2.150.28431310.20292820X-RAY DIFFRACTION98.63
2.15-2.20.26431300.20362830X-RAY DIFFRACTION99.33
2.2-2.250.24251250.1932836X-RAY DIFFRACTION99.33
2.25-2.310.23421230.18832808X-RAY DIFFRACTION99.29
2.31-2.370.19881220.18142840X-RAY DIFFRACTION99.16
2.37-2.440.22411280.18242860X-RAY DIFFRACTION99.1
2.44-2.520.20951330.17662811X-RAY DIFFRACTION98
2.52-2.610.24441580.18462710X-RAY DIFFRACTION96.89
2.61-2.710.21221450.18252841X-RAY DIFFRACTION99.7
2.71-2.840.22881380.18712833X-RAY DIFFRACTION99.7
2.84-2.990.23691570.19462822X-RAY DIFFRACTION99.33
2.99-3.170.21081670.18382814X-RAY DIFFRACTION99.37
3.17-3.420.20311630.16862750X-RAY DIFFRACTION97.46
3.42-3.760.18011500.1542841X-RAY DIFFRACTION99.57
3.76-4.310.17741310.13672872X-RAY DIFFRACTION99.24
4.31-5.420.13791480.13172817X-RAY DIFFRACTION98.18
5.42-39.290.2081520.17142899X-RAY DIFFRACTION98.39
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6732165845-0.6386740323821.119940693631.66032921935-0.0617442813882.05030594430.07403500765350.133396287654-0.167882493452-0.004863006294010.03305626430870.2166682410490.139886835472-0.150976607734-0.1117426196770.175628461649-0.03601866867140.009089295921360.2064279972670.02313595284720.22766628495710.37614.704-3.636
21.13247894115-0.3161045044790.4485190046281.03643638059-0.3772497120731.34066746519-0.004784951889610.04802975005030.06492790467720.0235617742901-0.0209799003817-0.103946906973-0.006581821149850.1423006302753.057389571250.156188520093-0.00816712068910.01282417656510.129436956309-0.007267172104620.14590579769140.41611.5878.982
32.342270186290.3268581395780.7484528787631.73363052817-0.3589726210591.67198460695-0.0592878735185-0.2020459857240.05834937480460.08793835774890.00296275887433-0.319189086690.01110315117140.06572760814680.04954613482180.1819820554480.03514073087330.004589664144630.263444490668-0.05578600200660.29654536573774.43917.08549.994
41.208163482080.1422024861460.3545009015131.154254152590.2374930397281.18088392761-0.0287094386366-0.165594609750.0668820220598-0.01265067606320.01589789794650.104204163207-0.0472021188635-0.08562911228080.0020726205020.161174799330.01054378546510.009048526766270.182899512851-0.001641104089480.13733886598544.32912.91337.415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:172 )A1 - 172
2X-RAY DIFFRACTION2( CHAIN A AND RESID 173:456 )A173 - 456
3X-RAY DIFFRACTION3( CHAIN B AND RESID 3:172 )B3 - 172
4X-RAY DIFFRACTION4( CHAIN B AND RESID 173:456 )B173 - 456

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