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- PDB-8oml: Crystal structure of Bdellovibrio bacteriovorus Bd1334 C-terminal... -

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Basic information

Entry
Database: PDB / ID: 8oml
TitleCrystal structure of Bdellovibrio bacteriovorus Bd1334 C-terminal domains
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / Fibre / Adhesin
Function / homologyPHOSPHATE ION / Cell wall surface anchor family protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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 31, 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5149
Polymers102,9453
Non-polymers5706
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30810 Å2
ΔGint-228 kcal/mol
Surface area29030 Å2
Unit cell
Length a, b, c (Å)196.738, 81.863, 58.850
Angle α, β, γ (deg.)90.00, 98.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell wall surface anchor family protein


Mass: 34314.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd1334 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MNC5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulphate, 0.1 M Imidazole/MES pH 6.5, 20 % v/v PEG 500 MME, 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→97.39 Å / Num. obs: 14282 / % possible obs: 47.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 8.5
Reflection shellResolution: 2.56→2.9 Å / Num. unique obs: 714 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→47.39 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 728 5.1 %
Rwork0.2151 --
obs0.2172 14264 47.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 30 73 7101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.187
X-RAY DIFFRACTIONf_dihedral_angle_d13.7912419
X-RAY DIFFRACTIONf_chiral_restr0.0691102
X-RAY DIFFRACTIONf_plane_restr0.0071293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.750.6311170.4289248X-RAY DIFFRACTION4
2.75-3.030.5013470.3448968X-RAY DIFFRACTION17
3.03-3.470.34611540.25872651X-RAY DIFFRACTION47
3.47-4.370.24472200.20294110X-RAY DIFFRACTION72
4.37-47.390.21952900.19925559X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 48.9737 Å / Origin y: 0.5623 Å / Origin z: 11.5533 Å
111213212223313233
T0.1701 Å2-0.0243 Å2-0.0274 Å2-0.1532 Å2-0.0353 Å2--0.093 Å2
L1.3971 °2-0.2189 °2-0.4087 °2-0.4753 °2-0.0271 °2--0.3009 °2
S-0.0096 Å °0.0439 Å °0.1114 Å °-0.0816 Å °-0.0143 Å °-0.121 Å °0.0056 Å °0.0039 Å °0.0234 Å °
Refinement TLS groupSelection details: all

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