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- PDB-9ea4: Structure of Citrobacter BubCD -

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Basic information

Entry
Database: PDB / ID: 9ea4
TitleStructure of Citrobacter BubCD
ComponentsCitrobacter BubCD
KeywordsLIGASE / ubiquitin / E1 / E2
Biological speciesCitrobacter sp. RHBSTW-00271 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0493
Polymers50,9611
Non-polymers882
Water9,602533
1
A: Citrobacter BubCD
hetero molecules

A: Citrobacter BubCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0986
Polymers101,9212
Non-polymers1774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4680 Å2
ΔGint-120 kcal/mol
Surface area36390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.498, 78.498, 159.295
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

21A-1032-

HOH

31A-1080-

HOH

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Components

#1: Protein Citrobacter BubCD


Mass: 50960.684 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.5, 0.2 M K/Na tartrate, 10% Isopropanol, 20% 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: 1.8→39.25 Å / Num. obs: 53524 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 22.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 9 % / Rmerge(I) obs: 1.423 / Num. unique obs: 3126 / CC1/2: 0.618 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.25 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.7301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1849 2730 5.11 %
Rwork0.1588 50705 -
obs0.1602 53435 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 2 533 4003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693531
X-RAY DIFFRACTIONf_angle_d0.84734780
X-RAY DIFFRACTIONf_chiral_restr0.0522546
X-RAY DIFFRACTIONf_plane_restr0.0107622
X-RAY DIFFRACTIONf_dihedral_angle_d11.88931305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.26741230.22852504X-RAY DIFFRACTION98.24
1.83-1.860.23671050.20012522X-RAY DIFFRACTION99.89
1.86-1.90.22951130.20522499X-RAY DIFFRACTION99.85
1.9-1.940.25451410.20642516X-RAY DIFFRACTION100
1.94-1.980.24321400.18512488X-RAY DIFFRACTION99.96
1.98-2.030.21291590.16532477X-RAY DIFFRACTION100
2.03-2.080.20891490.16372501X-RAY DIFFRACTION99.85
2.08-2.130.16621160.15272523X-RAY DIFFRACTION99.89
2.13-2.20.19061210.15892531X-RAY DIFFRACTION99.85
2.2-2.270.19581150.15042522X-RAY DIFFRACTION99.96
2.27-2.350.18641510.15132493X-RAY DIFFRACTION99.96
2.35-2.440.19211520.15132541X-RAY DIFFRACTION99.96
2.44-2.550.16891410.14662527X-RAY DIFFRACTION100
2.55-2.690.18141400.14812508X-RAY DIFFRACTION100
2.69-2.860.19681310.15722540X-RAY DIFFRACTION99.93
2.86-3.080.20051500.15132532X-RAY DIFFRACTION100
3.08-3.390.16751550.15132572X-RAY DIFFRACTION100
3.39-3.880.15331500.13942558X-RAY DIFFRACTION100
3.88-4.880.14361460.13762603X-RAY DIFFRACTION99.85
4.88-39.250.21671320.19152748X-RAY DIFFRACTION99.69
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)
12.316502036840.646228228530.3924212062281.881539433380.1699613578372.01523237870.0243766593912-0.380130097773-0.01367809327670.242632865643-0.0827438086187-0.04281770805160.008250742401930.03775894856830.04298485604930.141684986690.0107352906214-0.008938041985870.2275243950.01766199903640.13764943258225.338-3.719.054
21.15747466364-0.1728411524410.5074006454821.17200802347-0.0182865779131.22435529181-0.01594274109030.1361304494910.0617645716297-0.136648799151-0.0282128876556-0.0821402288219-0.03543980625190.1906880696820.02130537462260.113491555226-0.00949781178890.01244587523060.1432882604040.009323633495730.12236956323318.561-3.568-23.034
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 173:455 )A173 - 455

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