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- PDB-8oks: Crystal structure of Bdellovibrio bacteriovorus Bd2740 C-terminal... -

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Basic information

Entry
Database: PDB / ID: 8oks
TitleCrystal structure of Bdellovibrio bacteriovorus Bd2740 C-terminal domain
ComponentsPeptidase S74 domain-containing protein
KeywordsCELL ADHESION / Fibre / adhesin / C-type lectin
Function / homologyCell wall surface anchor family protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 29, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Peptidase S74 domain-containing protein
C: Peptidase S74 domain-containing protein
A: Peptidase S74 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)37,8483
Polymers37,8483
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-19 kcal/mol
Surface area12780 Å2
Unit cell
Length a, b, c (Å)51.084, 69.329, 87.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidase S74 domain-containing protein


Mass: 12616.068 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd2740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MJN2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 39.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 6.5, 40% PPGBA 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→44.11 Å / Num. obs: 12529 / % possible obs: 87 % / Redundancy: 5 % / CC1/2: 0.974 / Net I/σ(I): 7
Reflection shellResolution: 2.09→2.28 Å / Redundancy: 3.2 % / Num. unique obs: 626 / CC1/2: 0.349 / % possible all: 37

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→44.11 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 615 4.91 %
Rwork0.2265 --
obs0.2283 12517 66.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 0 40 2475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.736
X-RAY DIFFRACTIONf_dihedral_angle_d13.036859
X-RAY DIFFRACTIONf_chiral_restr0.05373
X-RAY DIFFRACTIONf_plane_restr0.004442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.310.4082320.3209720X-RAY DIFFRACTION16
2.31-2.640.30551110.31072590X-RAY DIFFRACTION58
2.64-3.320.27192210.25683968X-RAY DIFFRACTION89
3.32-44.110.2412510.18514624X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.4074 Å / Origin y: 13.9082 Å / Origin z: 18.0679 Å
111213212223313233
T0.1245 Å20.0056 Å2-0.0156 Å2-0.1468 Å20.0082 Å2--0.1503 Å2
L0.2646 °20.1902 °2-0.0186 °2-1.0927 °2-0.1278 °2--0.4268 °2
S0.008 Å °0.0313 Å °0.0371 Å °0.0129 Å °-0.0308 Å °-0.0082 Å °0.0047 Å °-0.0229 Å °0.0025 Å °
Refinement TLS groupSelection details: all

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