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- PDB-9eav: Structure of Citrobacter BubCD(D104A/Y370F)-BubB-BubA(155-229) -

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Basic information

Entry
Database: PDB / ID: 9eav
TitleStructure of Citrobacter BubCD(D104A/Y370F)-BubB-BubA(155-229)
Components
  • Citrobacter BubA
  • Citrobacter BubB
  • Citrobacter BubCD
KeywordsLIGASE / ubiquitin / E1 / E2
Function / homologyADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesCitrobacter sp. RHBSTW-00271 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 11, 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 BubA
D: Citrobacter BubB
E: Citrobacter BubB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3938
Polymers141,9995
Non-polymers3933
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.837, 136.837, 172.816
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
Components on special symmetry positions
IDModelComponents
11D-332-

TRP

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Components

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Protein , 3 types, 5 molecules ABCDE

#1: Protein Citrobacter BubCD


Mass: 50900.672 Da / Num. of mol.: 2 / Mutation: D104A, Y370F
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


Mass: 8807.037 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)
#3: Protein Citrobacter BubB


Mass: 15695.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RHBSTW-00271 (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 649 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.24 M sodium malonate pH 7.0 and 15% PEG 3350

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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: May 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.93→39.45 Å / Num. obs: 123100 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 1.855 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6024 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→34.21 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4676
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2036 6236 5.07 %
Rwork0.1831 116737 -
obs0.1842 122973 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.98 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9680 0 25 646 10351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01479901
X-RAY DIFFRACTIONf_angle_d1.232213435
X-RAY DIFFRACTIONf_chiral_restr0.0721512
X-RAY DIFFRACTIONf_plane_restr0.0181746
X-RAY DIFFRACTIONf_dihedral_angle_d12.83833656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.31472120.29593844X-RAY DIFFRACTION99.95
1.95-1.970.28131710.2663869X-RAY DIFFRACTION99.9
1.97-20.27561960.2453856X-RAY DIFFRACTION99.98
2-2.020.2391960.22993835X-RAY DIFFRACTION99.95
2.02-2.050.23832340.22183803X-RAY DIFFRACTION100
2.05-2.080.23022270.21813862X-RAY DIFFRACTION100
2.08-2.110.26551950.21883854X-RAY DIFFRACTION100
2.11-2.140.22132140.2193844X-RAY DIFFRACTION99.98
2.14-2.170.27042120.21053831X-RAY DIFFRACTION100
2.17-2.210.23452210.20473833X-RAY DIFFRACTION100
2.21-2.250.23292500.1973807X-RAY DIFFRACTION99.93
2.25-2.290.21141880.19453865X-RAY DIFFRACTION100
2.29-2.330.21612130.19933862X-RAY DIFFRACTION100
2.33-2.380.2411990.2023875X-RAY DIFFRACTION100
2.38-2.430.25371890.1973876X-RAY DIFFRACTION100
2.43-2.490.23352130.19243877X-RAY DIFFRACTION99.98
2.49-2.550.21842180.19873836X-RAY DIFFRACTION100
2.55-2.620.28351890.20163915X-RAY DIFFRACTION100
2.62-2.70.20982200.2053854X-RAY DIFFRACTION99.98
2.7-2.780.23781920.20523893X-RAY DIFFRACTION100
2.78-2.880.22572130.19933896X-RAY DIFFRACTION100
2.88-30.21391910.19943899X-RAY DIFFRACTION100
3-3.130.21312040.19293908X-RAY DIFFRACTION100
3.13-3.30.21142140.1963900X-RAY DIFFRACTION100
3.3-3.510.2022160.17093943X-RAY DIFFRACTION100
3.51-3.780.1571900.16133933X-RAY DIFFRACTION100
3.78-4.160.17182060.15423969X-RAY DIFFRACTION100
4.16-4.760.17072020.1473983X-RAY DIFFRACTION99.93
4.76-5.990.1792260.16024016X-RAY DIFFRACTION99.98
5.99-34.210.19862250.19194199X-RAY DIFFRACTION99.53
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)
11.36738694363-0.411826908595-0.3935497873421.60048955061.041018439741.035764163440.206224895775-0.4255063369980.677715811535-0.03518356513870.0295346396277-0.0523396374638-0.3319943769180.0965116478913-0.1277052342370.778408550055-0.07044221613210.2217088272980.635574498799-0.3129134972960.77616192097327.8620713932-6.4791966480735.4856061103
20.9827113986920.0892130303512-0.03316375955671.335654455680.01108308112050.8443212887440.0679100323927-0.2027033378040.04992782364480.245233228249-0.0772922317417-0.0263432998796-0.02893650596840.0908902500890.01177945531170.403814613967-0.0001863933534740.00201334057980.32309941691-0.01086767024120.27642880733236.9563732115-32.941484042315.303178467
31.23220822309-0.279416839994-0.2486662600463.086687563531.144100387181.9164471910.02903157960940.178610087726-0.244090669853-0.217065259103-0.06105858763680.08469302585140.1279458108540.03749107891130.06984051830890.4318054173790.08270506541090.0007512568158430.28427140089-0.02751937425620.38446553351924.1167398334-63.2028218478-27.1705785533
40.9253048574890.1407871171670.4256935353810.7595135640240.07111470073451.19802809996-0.0130864640898-0.01002806629160.145161476611-0.0204442102823-0.018906776990.0723969655059-0.096546315656-0.03657698703530.03573433790980.304012082090.03670663755960.01216705100390.2250468592960.01882905050340.29651126261922.180094984-32.5906218788-11.3750074624
51.18275298267-0.100305757542-0.9605979998461.84928993005-0.3945212210411.45976298718-0.105268170384-0.23830126223-0.06595726812020.4283749272340.06346820707240.679545673834-0.0514137128514-0.267542172221-0.005858543983050.6674053385920.003069016123550.05926072899960.6361693122350.07103380986250.7526318426319.6767391582-57.303135248718.248757342
63.06252682550.0790610431301-0.02407177454062.034929898630.05586630539861.75771716275-0.1282960909060.373566139660.244075512882-0.180160660190.09587637166740.134309789685-0.181644983434-0.1261748414530.03049669867340.370202348325-0.0248676376425-0.05989924808140.3309193809330.07803612139580.3192577185130.376242449037-21.3443127987-36.3085296708
71.43915224338-0.03114739445460.4411612113031.39981801459-0.1455118159991.188135327760.270547706952-0.0421631776133-0.3632204442730.55789358066-0.171234086378-0.1480953463060.1122836005690.375001877145-0.02084287276580.758218915347-0.149718497452-0.1329105628150.631045211147-0.008287754403460.42274652269855.9833241843-46.264010607541.4716464111
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 0:172AA4 - 1721 - 166
22chain A and resid 173:456AA173 - 456167 - 450
33chain B and resid 0:172BC4 - 1721 - 164
44chain B and resid 173:456BC173 - 456165 - 448
55chain CCF1 - 751 - 75
66chain EEH234 - 3611 - 128
77chain DDG234 - 3611 - 128

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