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- PDB-9ea8: Citrobacter BubCD(D104A)-BubA(155-229) complex -

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Basic information

Entry
Database: PDB / ID: 9ea8
TitleCitrobacter BubCD(D104A)-BubA(155-229) complex
Components
  • Citrobacter BubA 155-229
  • Citrobacter BubCD D104A
KeywordsLIGASE / ubiquitin / E1 / DUB
Biological speciesCitrobacter sp. RHBSTW-00271 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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: To Be Published
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. / Corbett, K.D.
History
DepositionNov 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrobacter BubCD D104A
B: Citrobacter BubA 155-229


Theoretical massNumber of molelcules
Total (without water)59,7242
Polymers59,7242
Non-polymers00
Water1,44180
1
A: Citrobacter BubCD D104A
B: Citrobacter BubA 155-229

A: Citrobacter BubCD D104A
B: Citrobacter BubA 155-229


Theoretical massNumber of molelcules
Total (without water)119,4474
Polymers119,4474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)96.636, 96.636, 135.204
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 Citrobacter BubCD D104A


Mass: 50916.672 Da / Num. of mol.: 1 / 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: Protein Citrobacter BubA 155-229


Mass: 8807.037 Da / Num. of mol.: 1 / Fragment: residues 155-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RHBSTW-00271 (bacteria)
Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.0, 2.2 M sodium acetate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.34→39.31 Å / Num. obs: 27750 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 63.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.8
Reflection shellResolution: 2.34→2.42 Å / Rmerge(I) obs: 1.634 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2663 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→39.31 Å / SU ML: 0.3237 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.7916
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 1396 5.04 %
Rwork0.2378 26290 -
obs0.2393 27686 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.85 Å2
Refinement stepCycle: LAST / Resolution: 2.34→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 0 80 4217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384213
X-RAY DIFFRACTIONf_angle_d0.6115705
X-RAY DIFFRACTIONf_chiral_restr0.0444651
X-RAY DIFFRACTIONf_plane_restr0.0078742
X-RAY DIFFRACTIONf_dihedral_angle_d14.45371569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.420.34061310.30792570X-RAY DIFFRACTION100
2.42-2.520.32541790.29892541X-RAY DIFFRACTION99.96
2.52-2.640.39651180.35122600X-RAY DIFFRACTION99.89
2.64-2.770.38141270.31952609X-RAY DIFFRACTION100
2.77-2.950.25311400.29332578X-RAY DIFFRACTION100
2.95-3.180.35731280.30412617X-RAY DIFFRACTION99.96
3.18-3.490.30751320.26252632X-RAY DIFFRACTION100
3.5-40.27781460.22532644X-RAY DIFFRACTION100
4-5.040.22831470.18072675X-RAY DIFFRACTION100
5.04-39.310.22921480.21982824X-RAY DIFFRACTION99.93
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)
12.509575673590.820417172172-0.3958301477753.26526495715-0.07458947528522.33087175034-0.109168121177-0.154752083646-0.266212159263-0.325989949240.3727309315850.7491816798970.374046954919-0.661493435226-0.3536918885460.623825824782-0.102046654388-0.180993608480.7746811630230.2366287478450.862924571692-16.844-41.07842.267
21.595225645660.634582012646-0.318189598342.11701506218-1.044655220762.282336685510.129459736905-0.2297567004690.1235652934920.285810439580.1184000485310.188531516605-0.246643016245-0.125365133686-0.2442473634780.4754336792740.06446718667760.0004840237063550.535830217856-0.02280799608180.4484937158883.872-14.42947.176
32.80041404993-1.576143376530.9424663941642.0043719804-2.295656744083.09989395084-0.027988836841-0.668650920715-0.4559376830710.2511299783660.0284942690766-0.452441417479-0.01231021600550.5383796680380.08557518768420.8520635424390.0236691222271-0.108241855581.1579945149-0.01087274547160.96124719432533.397-19.80650.627
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 155:229 )B155 - 229

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