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- PDB-8ond: Structure of the C-terminal domains of the Bdellovibrio bacteriov... -

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Basic information

Entry
Database: PDB / ID: 8ond
TitleStructure of the C-terminal domains 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: 2.5 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
DepositionApr 2, 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
B: bd2133
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5438
Polymers76,3562
Non-polymers1886
Water1,67593
1
A: bd2133
hetero molecules

A: bd2133
hetero molecules

A: bd2133
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,81512
Polymers114,5333
Non-polymers2829
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area35210 Å2
ΔGint-238 kcal/mol
Surface area33420 Å2
MethodPISA
2
B: bd2133
hetero molecules

B: bd2133
hetero molecules

B: bd2133
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,81512
Polymers114,5333
Non-polymers2829
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area35270 Å2
ΔGint-246 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.308, 65.308, 319.187
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1101-

CL

21A-1102-

CL

31A-1103-

NA

41B-1101-

CL

51B-1102-

CL

61B-1103-

NA

71A-1202-

HOH

81B-1204-

HOH

91B-1244-

HOH

101B-1249-

HOH

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Components

#1: Protein bd2133


Mass: 38177.832 Da / Num. of mol.: 2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.03 M sodium fluoride, 0.03M sodium bromide, 0.03M sodium iodide, 0.1 M imidazole/MES pH 6.5, 20 % v/v glycerol, 10 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→55.69 Å / Num. obs: 26645 / % possible obs: 100 % / Redundancy: 42.4 % / CC1/2: 1 / Net I/σ(I): 24.5
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2990 / CC1/2: 0.896

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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: 2.5→46.14 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1332 5.02 %
Rwork0.2003 --
obs0.2017 26556 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 6 93 5160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075199
X-RAY DIFFRACTIONf_angle_d0.9767093
X-RAY DIFFRACTIONf_dihedral_angle_d12.7491770
X-RAY DIFFRACTIONf_chiral_restr0.061827
X-RAY DIFFRACTIONf_plane_restr0.006930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.35591230.27922522X-RAY DIFFRACTION100
2.59-2.690.33721410.26052514X-RAY DIFFRACTION100
2.69-2.810.29471430.26722505X-RAY DIFFRACTION100
2.81-2.960.30091180.23722548X-RAY DIFFRACTION100
2.96-3.150.29431130.24322541X-RAY DIFFRACTION100
3.15-3.390.21111310.22582507X-RAY DIFFRACTION100
3.39-3.730.21461540.19492488X-RAY DIFFRACTION100
3.73-4.270.22911200.17712553X-RAY DIFFRACTION100
4.27-5.380.1821340.15932538X-RAY DIFFRACTION100
5.38-46.140.21191550.19722508X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -31.6237 Å / Origin y: 2.772 Å / Origin z: -1.1514 Å
111213212223313233
T0.401 Å2-0.0275 Å20.0172 Å2-0.4867 Å2-0.0103 Å2--0.5895 Å2
L-0.0539 °2-0.0221 °20.016 °2--0.0374 °20.0472 °2--0.6272 °2
S-0.0235 Å °0.0066 Å °0.0314 Å °0.011 Å °-0.0517 Å °0.0019 Å °0.0051 Å °-0.024 Å °0.0786 Å °
Refinement TLS groupSelection details: all

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