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- PDB-8ok3: Structure of the C-terminal domain of the Bdellovibrio bacteriovo... -

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Basic information

Entry
Database: PDB / ID: 8ok3
TitleStructure of the C-terminal domain of the Bdellovibrio bacteriovorus Bd2133 fibre
ComponentsBd2133
KeywordsCELL ADHESION / Fibre / adhesin
Function / homologyCell wall surface anchor family protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCaulton, S.G. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209437/Z/17/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2024
Title: Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts.
Authors: Caulton, S.G. / Lambert, C. / Tyson, J. / Radford, P. / Al-Bayati, A. / Greenwood, S. / Banks, E.J. / Clark, C. / Till, R. / Pires, E. / Sockett, R.E. / Lovering, A.L.
History
DepositionMar 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bd2133
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4265
Polymers13,2361
Non-polymers1904
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-37 kcal/mol
Surface area6030 Å2
Unit cell
Length a, b, c (Å)68.760, 68.760, 68.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1101-

SO4

21A-1101-

SO4

31A-1102-

NA

41A-1104-

CL

51A-1201-

HOH

61A-1202-

HOH

71A-1212-

HOH

81A-1317-

HOH

91A-1330-

HOH

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Components

#1: Protein Bd2133


Mass: 13235.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd2133 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ML84
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.03M magnesium chloride, 0.03M calcium chloride, 0.1 M imidazole/MES pH 6.5, 12.5 % v/v MPD, 12.5 % PEG 1000, 12.5 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→30.75 Å / Num. obs: 17441 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.996 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.4 % / Num. unique obs: 1266 / CC1/2: 0.815 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.75 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1592 828 4.75 %
Rwork0.1503 --
obs0.1508 17441 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 0 8 130 1050
Refinement TLS params.Method: refined / Origin x: 13.3515 Å / Origin y: 19.0648 Å / Origin z: 1.8519 Å
111213212223313233
T0.1128 Å2-0.0033 Å20.0046 Å2-0.1061 Å20.0023 Å2--0.1108 Å2
L0.2941 °2-0.1958 °2-0.0779 °2-0.2247 °2-0.1196 °2--0.5146 °2
S0.0167 Å °0.0184 Å °0.0348 Å °-0.0359 Å °-0.0045 Å °-0.0327 Å °-0.0833 Å °-0.0021 Å °-0.0063 Å °
Refinement TLS groupSelection details: all

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