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- PDB-9eae: Structure of Citrobacter BubCD(D104A)-BubB -

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Basic information

Entry
Database: PDB / ID: 9eae
TitleStructure of Citrobacter BubCD(D104A)-BubB
Components
  • Citrobacter BubB
  • Citrobacter BubCD
KeywordsLIGASE / ubiquitin / E1 / DUB / E2
Biological speciesCitrobacter sp. RHBSTW-00271 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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
B: Citrobacter BubCD
C: Citrobacter BubB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3035
Polymers117,2573
Non-polymers462
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-49 kcal/mol
Surface area42590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.350, 135.350, 172.797
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


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: Protein Citrobacter BubB


Mass: 15423.288 Da / Num. of mol.: 1 / Fragment: residues 230-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RHBSTW-00271 (bacteria)
Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium cacodylate pH 7.0, 0.2 M MgCl2, 10% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.526→106.554 Å / Num. obs: 54407 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 66.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.2
Reflection shellResolution: 2.526→2.569 Å / Rmerge(I) obs: 1.759 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2638 / CC1/2: 0.757

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→49.35 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.2407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 2778 5.11 %
Rwork0.2464 51596 -
obs0.2476 54374 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.16 Å2
Refinement stepCycle: LAST / Resolution: 2.53→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8108 0 2 156 8266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00258264
X-RAY DIFFRACTIONf_angle_d0.520511201
X-RAY DIFFRACTIONf_chiral_restr0.04331267
X-RAY DIFFRACTIONf_plane_restr0.01151460
X-RAY DIFFRACTIONf_dihedral_angle_d15.16733055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.570.43331120.41612524X-RAY DIFFRACTION99.92
2.57-2.620.39231520.4032552X-RAY DIFFRACTION99.93
2.62-2.670.39871550.35372507X-RAY DIFFRACTION99.89
2.67-2.720.34821460.3372528X-RAY DIFFRACTION100
2.72-2.780.35651370.31662547X-RAY DIFFRACTION99.93
2.78-2.840.331240.31462548X-RAY DIFFRACTION100
2.84-2.920.29491300.30932555X-RAY DIFFRACTION99.96
2.92-2.990.32831310.31662564X-RAY DIFFRACTION99.78
2.99-3.080.31471410.31572561X-RAY DIFFRACTION99.93
3.08-3.180.39391490.34352533X-RAY DIFFRACTION99.89
3.18-3.30.34691240.30452576X-RAY DIFFRACTION99.96
3.3-3.430.32231320.26652565X-RAY DIFFRACTION100
3.43-3.580.27321440.25342566X-RAY DIFFRACTION100
3.58-3.770.27071330.25072595X-RAY DIFFRACTION100
3.77-4.010.24091440.22712570X-RAY DIFFRACTION99.96
4.01-4.320.21611460.19942596X-RAY DIFFRACTION100
4.32-4.750.1991450.18272593X-RAY DIFFRACTION99.96
4.75-5.440.22171520.19032624X-RAY DIFFRACTION99.93
5.44-6.850.25971370.24112679X-RAY DIFFRACTION100
6.85-49.350.27461440.22842813X-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)
11.60724711226-0.1270518168060.4755192360765.06967512294-2.045232234984.482517776770.05959333643190.198691111660.4098684193360.0156351655836-0.04607853747510.220966920168-0.206710246715-0.08423818921020.005340224909040.5791757373380.105801235557-0.1564119638480.5093681008680.02219532358860.72789160759744.199-6.303-27.436
21.484522598780.0303680744918-0.5865054605831.76838614446-0.6242724464392.34871669530.04327154673730.0445718440746-0.1456459655570.0442524800491-0.0747115553912-0.1460811232970.0537103433310.1807610920370.04641932985670.5170722273810.0547233741487-0.1476855802650.483548823575-0.07172329448780.56581927313946.136-36.341-11.24
33.31778343988-0.5896582584780.1888717576312.33746216948-1.874895890512.494541064790.666456599202-0.798956622905-1.32811929250.410084708567-0.298048402106-0.01672170101060.426315858886-0.0140812435182-0.2399418927261.18550690809-0.2739878375-0.5350288746650.6804789622040.3646146439781.1570176710439.368-61.83935.245
42.080130133330.07107515504970.1221333248982.250915695820.1416151031270.8449628157490.188637112884-0.168934973406-0.09120883897970.529088286392-0.0765972496856-0.007706091613970.102865595473-0.0742577783407-0.08918455538690.702086004267-0.0121035241985-0.07277904513330.509266275744-0.03937239861770.46414748657831.034-35.50915.389
53.134714091970.53972309244-0.6427016048372.21665803957-0.193136188993.67915384838-0.2590096592740.486873991983-0.664662621047-0.3728658455220.1757481415470.02213754536350.318926363145-0.01930464997160.0983374067460.551104874005-0.0514458872447-0.01383287404290.566303611426-0.194635133880.71473706964468.815-47.586-35.467
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 2:172 )B2 - 172
4X-RAY DIFFRACTION4( CHAIN B AND RESID 173:456 )B173 - 456
5X-RAY DIFFRACTION5( CHAIN C AND RESID 234:361 )C234 - 361

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