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- PDB-8ol4: Structure of the C-terminal domains of the Bdellovibrio bacteriov... -

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Basic information

Entry
Database: PDB / ID: 8ol4
TitleStructure of the C-terminal domains of the Bdellovibrio bacteriovorus Bd2439 fibre in complex with GlcNAc
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / Fibre / adhesin / TNF / TNF-like
Function / homologyIODIDE ION / DI(HYDROXYETHYL)ETHER / Cell wall surface anchor family protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 30, 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)93,04816
Polymers91,0063
Non-polymers2,04113
Water10,467581
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23360 Å2
ΔGint-90 kcal/mol
Surface area25270 Å2
Unit cell
Length a, b, c (Å)84.219, 160.345, 52.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Cell wall surface anchor family protein


Mass: 30335.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd2439 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MKF5
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 591 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.93 Å3/Da / Density % sol: 36.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane pH 8.5, 20 % w/v PEG 3350, 100 mM GlcNAc-MurNAc

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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: 1.84→80.17 Å / Num. obs: 49745 / % possible obs: 80.2 % / Redundancy: 11.8 % / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 1.84→1.98 Å / Num. unique obs: 2487 / CC1/2: 0.664

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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: 1.84→45.13 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 2473 4.97 %
Rwork0.1656 --
obs0.1672 49729 80.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 113 581 6382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.936
X-RAY DIFFRACTIONf_dihedral_angle_d12.3762170
X-RAY DIFFRACTIONf_chiral_restr0.06951
X-RAY DIFFRACTIONf_plane_restr0.0091077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.262440.264139X-RAY DIFFRACTION4
1.88-1.910.2994220.2531492X-RAY DIFFRACTION15
1.91-1.960.2594510.2259906X-RAY DIFFRACTION28
1.96-20.2416940.21761411X-RAY DIFFRACTION44
2-2.050.26981030.21042199X-RAY DIFFRACTION68
2.05-2.110.21061640.22758X-RAY DIFFRACTION85
2.11-2.170.22631630.18453049X-RAY DIFFRACTION94
2.17-2.240.20881970.17633158X-RAY DIFFRACTION99
2.24-2.320.19141540.17223260X-RAY DIFFRACTION100
2.32-2.410.22651650.17883262X-RAY DIFFRACTION100
2.41-2.520.23341680.17463258X-RAY DIFFRACTION100
2.52-2.650.231590.18353276X-RAY DIFFRACTION100
2.65-2.820.21441690.16583275X-RAY DIFFRACTION100
2.82-3.040.17521780.16643290X-RAY DIFFRACTION100
3.04-3.340.17971690.1623293X-RAY DIFFRACTION100
3.34-3.830.1771540.13933354X-RAY DIFFRACTION100
3.83-4.820.15221610.13223368X-RAY DIFFRACTION100
4.82-45.130.21421980.18413508X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.9184 Å / Origin y: 21.4548 Å / Origin z: 12.7431 Å
111213212223313233
T0.1886 Å20.0014 Å20.0125 Å2-0.1584 Å2-0.0097 Å2--0.1575 Å2
L0.6619 °20.162 °20.1649 °2-0.2609 °20.0636 °2--0.179 °2
S-0.0142 Å °0.0678 Å °-0.0087 Å °-0.0283 Å °0.0205 Å °-0.0025 Å °0.0033 Å °-0.0113 Å °-0.0039 Å °
Refinement TLS groupSelection details: all

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