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- PDB-5xbj: The structure of the flagellar hook junction protein HAP1 (FlgK) ... -

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Basic information

Entry
Database: PDB / ID: 5xbj
TitleThe structure of the flagellar hook junction protein HAP1 (FlgK) from Campylobacter jejuni
ComponentsFlagellar hook-associated protein FlgK
KeywordsBIOSYNTHETIC PROTEIN / Bacterial Flagellum / Hook / Filament / Junction protein
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 1 / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
: / Flagellar hook-associated protein 1
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.448 Å
AuthorsSamatey, F.A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Okinawa Institute of Science and Technology Graduate University Japan
CitationJournal: Sci Rep / Year: 2017
Title: Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter
Authors: Bulieris, P.V. / Shaikh, N.H. / Freddolino, P.L. / Samatey, F.A.
History
DepositionMar 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 FlgK


Theoretical massNumber of molelcules
Total (without water)56,9831
Polymers56,9831
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Based on the assembly of the bacterial flagellum, the protein makes an 11-mer to form HAP1 (Hook Associated Protein 1)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24150 Å2
Unit cell
Length a, b, c (Å)49.501, 123.552, 92.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 11 / Rise per n subunits: 4.185 Å / Rotation per n subunits: 64.34 °)
Components on special symmetry positions
IDModelComponents
11A-984-

HOH

21A-999-

HOH

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Components

#1: Protein Flagellar hook-associated protein FlgK


Mass: 56983.164 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRK1T (others)
References: UniProt: A0A218KZD0, UniProt: Q0P8E9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG MME 2000, 0.4M AMMONIUM, ACETATE, 2% MPD, 4% 2-PROPANOL, 5% ETHYLENE GLYCOL, 0.1M SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.45→38.62 Å / Num. obs: 21573 / % possible obs: 99.76 % / Redundancy: 7.3 % / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D4Y

2d4y


Resolution: 2.448→19.971 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 1927 9.26 %
Rwork0.1785 --
obs0.1834 20801 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.448→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 0 399 4322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033979
X-RAY DIFFRACTIONf_angle_d0.5175378
X-RAY DIFFRACTIONf_dihedral_angle_d13.3992421
X-RAY DIFFRACTIONf_chiral_restr0.04598
X-RAY DIFFRACTIONf_plane_restr0.003716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4485-2.50960.28771270.2121219X-RAY DIFFRACTION89
2.5096-2.57730.28731270.20931273X-RAY DIFFRACTION93
2.5773-2.6530.25561300.19061283X-RAY DIFFRACTION94
2.653-2.73840.26961320.19871293X-RAY DIFFRACTION94
2.7384-2.8360.28421320.19041302X-RAY DIFFRACTION95
2.836-2.94920.24571380.18531329X-RAY DIFFRACTION96
2.9492-3.0830.25971400.18931355X-RAY DIFFRACTION97
3.083-3.24490.22361380.17681340X-RAY DIFFRACTION97
3.2449-3.44720.22011410.17221369X-RAY DIFFRACTION98
3.4472-3.71180.1961420.16081370X-RAY DIFFRACTION99
3.7118-4.08240.25471400.15831393X-RAY DIFFRACTION99
4.0824-4.66660.20441440.14641408X-RAY DIFFRACTION100
4.6666-5.85480.21151430.17911437X-RAY DIFFRACTION99
5.8548-19.97190.19641530.19981503X-RAY DIFFRACTION99

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