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- PDB-8on4: Structure of the C-terminal domains of the Bdellovibrio bacteriov... -

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Basic information

Entry
Database: PDB / ID: 8on4
TitleStructure of the C-terminal domains of the Bdellovibrio bacteriovorus Bd1334 fibre
ComponentsCell wall surface anchor family protein
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: 1.41 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 6, 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
A: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)24,6571
Polymers24,6571
Non-polymers00
Water3,315184
1
A: Cell wall surface anchor family protein

A: Cell wall surface anchor family protein

A: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)73,9723
Polymers73,9723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12320 Å2
ΔGint-86 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.940, 82.940, 67.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1324-

HOH

21A-1342-

HOH

31A-1377-

HOH

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Components

#1: Protein Cell wall surface anchor family protein


Mass: 24657.205 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.82 Å3/Da / Density % sol: 32.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium chloride, 0.1 M MES pH 6.0, 20 % w/v PEG 6000

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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 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.41→41.47 Å / Num. obs: 30502 / % possible obs: 91.1 % / Redundancy: 9 % / CC1/2: 1 / Net I/σ(I): 22.2
Reflection shellResolution: 1.41→1.45 Å / Num. unique obs: 1320 / CC1/2: 0.395

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→41.47 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 1461 5.11 %
Rwork0.171 --
obs0.1725 28580 85.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 0 184 1687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.022
X-RAY DIFFRACTIONf_dihedral_angle_d14.431529
X-RAY DIFFRACTIONf_chiral_restr0.094234
X-RAY DIFFRACTIONf_plane_restr0.008281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.460.3462620.36551434X-RAY DIFFRACTION45
1.46-1.520.37991000.31281955X-RAY DIFFRACTION62
1.52-1.590.3231310.27652376X-RAY DIFFRACTION75
1.59-1.670.23861350.22682829X-RAY DIFFRACTION89
1.67-1.780.23681830.18772913X-RAY DIFFRACTION92
1.78-1.910.19871570.17393039X-RAY DIFFRACTION95
1.91-2.110.18281750.17423086X-RAY DIFFRACTION97
2.11-2.410.21911850.17663126X-RAY DIFFRACTION99
2.41-3.040.19631510.17793188X-RAY DIFFRACTION100
3.04-41.470.17851820.14633173X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.18641.37791.1544.17041.10811.78250.0438-0.820.6110.865-0.17810.0789-0.53880.4439-0.00920.5548-0.11450.00310.5363-0.14890.27118.306610.7988-6.6144
21.93410.0914-0.54157.00730.41552.39040.0629-0.3185-0.14590.63290.1437-0.9360.55410.5782-0.20130.4420.0429-0.13420.3865-0.02340.24710.9449-3.973-11.4258
31.17230.1970.15341.33760.42271.10970.0487-0.0608-0.12530.0364-0.01670.12770.0676-0.1206-0.00370.1294-0.00070.01870.12350.01640.1782-6.1478-4.2729-34.2056
43.26794.1333-1.59095.3031-2.2111.68910.56120.19230.5303-0.1806-0.04851.18-0.2769-0.381-0.37210.3173-0.0443-0.08930.4095-0.00010.472-18.1785-4.6993-59.8947
51.7504-0.3211-0.36181.71070.87851.74630.03880.195-0.1387-0.1664-0.08870.28080.0525-0.21390.02190.1482-0.0114-0.03610.1468-0.01550.2168-10.6986-7.4201-50.9271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 948 through 965 )
2X-RAY DIFFRACTION2chain 'A' and (resid 966 through 980 )
3X-RAY DIFFRACTION3chain 'A' and (resid 981 through 1056 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1057 through 1069 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1070 through 1151 )

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