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- PDB-6ndw: Crystal structure of the wild type D2 domain (A168-T344) of the f... -

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Basic information

Entry
Database: PDB / ID: 6ndw
TitleCrystal structure of the wild type D2 domain (A168-T344) of the flagellar hook protein FlgE from Treponema denticola
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / hook / lysinoalanine / crosslinking / spirochetes / periodontal disease / FlgE
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytosol
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal ...Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.725 Å
AuthorsLynch, M.J. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35-122535 United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structure and chemistry of lysinoalanine crosslinking in the spirochaete flagella hook.
Authors: Lynch, M.J. / Miller, M. / James, M. / Zhang, S. / Zhang, K. / Li, C. / Charon, N.W. / Crane, B.R.
History
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
B: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)19,1211
Polymers19,1211
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.104, 61.290, 43.790
Angle α, β, γ (deg.)90.00, 104.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagellar hook protein FlgE


Mass: 19120.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: flgE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RQB6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.725→50 Å / Num. obs: 17865 / % possible obs: 99.6 % / Redundancy: 6.6 % / Net I/σ(I): 24.5
Reflection shellResolution: 1.73→1.78 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WLG

1wlg


Resolution: 1.725→24.838 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 1786 10 %random selection
Rwork0.1589 ---
obs0.1617 17858 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.725→24.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 249 1587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061363
X-RAY DIFFRACTIONf_angle_d0.7751862
X-RAY DIFFRACTIONf_dihedral_angle_d12.668803
X-RAY DIFFRACTIONf_chiral_restr0.055215
X-RAY DIFFRACTIONf_plane_restr0.005250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7247-1.77130.2331290.17581167X-RAY DIFFRACTION94
1.7713-1.82340.21721380.17211244X-RAY DIFFRACTION100
1.8234-1.88220.21971380.16931237X-RAY DIFFRACTION100
1.8822-1.94950.20261360.16161222X-RAY DIFFRACTION100
1.9495-2.02750.19281360.15231234X-RAY DIFFRACTION100
2.0275-2.11970.17681370.14971228X-RAY DIFFRACTION100
2.1197-2.23140.19011380.15011242X-RAY DIFFRACTION100
2.2314-2.37110.18091390.15921248X-RAY DIFFRACTION100
2.3711-2.5540.18051380.15611243X-RAY DIFFRACTION100
2.554-2.81070.20281370.17021242X-RAY DIFFRACTION100
2.8107-3.21670.17881390.15851241X-RAY DIFFRACTION100
3.2167-4.04990.17861380.14491253X-RAY DIFFRACTION100
4.0499-24.84060.1761430.1681271X-RAY DIFFRACTION100

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