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- PDB-6kty: Crystal structure of the flagellar cap protein FliD from Bdellovi... -

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Basic information

Entry
Database: PDB / ID: 6kty
TitleCrystal structure of the flagellar cap protein FliD from Bdellovibrio bacteriovorus
ComponentsFlagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Bacterial flagellar cap protein
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus
Similarity search - Domain/homology
Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsCho, S.Y. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2019R1A2C1002100 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of the flagellar cap protein FliD from Bdellovibrio bacteriovorus.
Authors: Cho, S.Y. / Song, W.S. / Yoon, S.I.
History
DepositionAug 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)21,2191
Polymers21,2191
Non-polymers00
Water97354
1
A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)84,8754
Polymers84,8754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9110 Å2
ΔGint-20 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.811, 97.811, 83.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein


Mass: 21218.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: fliD, Bd0610 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6MQ71
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: ammonium sulfate, MES, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 13863 / % possible obs: 98 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 46.5
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 694 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25733 682 -
Rwork0.21593 --
obs0.21801 13174 98 %
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 0 54 1385
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 60 -
Rwork0.247 949 -
obs--99.61 %
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)
13.4227-1.2124-0.25351.3905-0.1630.75850.1362-0.02910.29450.0261-0.0604-0.0551-0.13970.0446-0.07580.1209-0.0326-0.01610.0819-0.03510.171313.78910.46213.947
24.235-2.7821-0.17757.4854-0.08370.7432-0.02430.14570.05950.1861-0.0733-0.50450.05070.11690.09750.1094-0.0027-0.02290.1715-0.01660.096133.75-2.7112.541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A74 - 105
2X-RAY DIFFRACTION1A186 - 256
3X-RAY DIFFRACTION2A106 - 185

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