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- PDB-8onc: Structure of the C-terminal beta helix domain of the Bdellovibrio... -

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Basic information

Entry
Database: PDB / ID: 8onc
TitleStructure of the C-terminal beta helix domain of the Bdellovibrio bacteriovorus Bd3182 fibre
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / Fibre / adhesin
Function / homologyIntramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Cell wall surface anchor family protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionApr 1, 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: Cell wall surface anchor family protein
E: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein
D: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein
F: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1767
Polymers93,1146
Non-polymers621
Water10,269570
1
A: Cell wall surface anchor family protein
C: Cell wall surface anchor family protein
B: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)46,5573
Polymers46,5573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18480 Å2
ΔGint-102 kcal/mol
Surface area14740 Å2
2
E: Cell wall surface anchor family protein
D: Cell wall surface anchor family protein
F: Cell wall surface anchor family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6194
Polymers46,5573
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-96 kcal/mol
Surface area14750 Å2
Unit cell
Length a, b, c (Å)111.457, 48.153, 172.204
Angle α, β, γ (deg.)90.00, 107.11, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Cell wall surface anchor family protein


Mass: 15519.053 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd3182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MIH5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→79.41 Å / Num. obs: 59598 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 4316 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→79.41 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 3052 5.13 %
Rwork0.1762 --
obs0.1776 59481 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→79.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 4 570 6894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.67
X-RAY DIFFRACTIONf_dihedral_angle_d11.592163
X-RAY DIFFRACTIONf_chiral_restr0.0521070
X-RAY DIFFRACTIONf_plane_restr0.0041148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.25461410.22842528X-RAY DIFFRACTION100
2.03-2.060.27681150.21452582X-RAY DIFFRACTION100
2.06-2.10.23891470.21582522X-RAY DIFFRACTION100
2.1-2.140.24541380.20242515X-RAY DIFFRACTION100
2.14-2.180.23261280.19592576X-RAY DIFFRACTION100
2.18-2.220.25621080.19452575X-RAY DIFFRACTION100
2.22-2.270.27261630.20942518X-RAY DIFFRACTION99
2.27-2.330.26551380.19642530X-RAY DIFFRACTION100
2.33-2.380.20571390.18062546X-RAY DIFFRACTION100
2.38-2.450.2211230.18972549X-RAY DIFFRACTION100
2.45-2.520.22781450.1962571X-RAY DIFFRACTION100
2.52-2.60.21771370.19722545X-RAY DIFFRACTION100
2.6-2.690.26711310.1982572X-RAY DIFFRACTION100
2.69-2.80.19421390.19232546X-RAY DIFFRACTION100
2.8-2.930.21821680.18912550X-RAY DIFFRACTION100
2.93-3.080.22411520.18252545X-RAY DIFFRACTION100
3.08-3.280.17561460.16472582X-RAY DIFFRACTION100
3.28-3.530.18571190.16012582X-RAY DIFFRACTION100
3.53-3.890.17241380.14482605X-RAY DIFFRACTION100
3.89-4.450.14441450.13832592X-RAY DIFFRACTION100
4.45-5.60.16311430.1422598X-RAY DIFFRACTION99
5.6-79.410.21981490.20042700X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.7099 Å / Origin y: -7.187 Å / Origin z: 42.754 Å
111213212223313233
T0.1692 Å20.0192 Å2-0.0052 Å2-0.1046 Å2-0.017 Å2--0.1764 Å2
L0.5502 °20.2114 °2-0.1292 °2-0.3905 °2-0.1323 °2--0.2731 °2
S0.0094 Å °-0.0344 Å °-0.0239 Å °0.009 Å °-0.0149 Å °-0.0092 Å °-0.0188 Å °-0.0027 Å °-0.0008 Å °
Refinement TLS groupSelection details: all

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