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- PDB-6ndv: FlgE D2 domain K336A mutant -

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Basic information

Entry
Database: PDB / ID: 6ndv
TitleFlgE D2 domain K336A mutant
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / hook / lysinoalanine / crosslinking / spirochetes / periodontal disease / FlgE / dehydroalanine
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / 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 protein FlgE
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.502 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 21, 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 1.4Mar 13, 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

Downloads & links

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Assembly

Deposited unit
B: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)19,0631
Polymers19,0631
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.163, 61.344, 43.800
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagellar hook protein FlgE


Mass: 19062.682 Da / Num. of mol.: 1 / Mutation: K336A
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 / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 26374 / % possible obs: 97.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 10.15 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Net I/σ(I): 21.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6 % / Num. unique obs: 2568 / CC1/2: 0.95 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 1.502→34.892 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.65
RfactorNum. reflection% reflection
Rfree0.1777 2000 7.58 %
Rwork0.1581 --
obs0.1596 26374 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.502→34.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 0 283 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051359
X-RAY DIFFRACTIONf_angle_d0.781858
X-RAY DIFFRACTIONf_dihedral_angle_d7.182799
X-RAY DIFFRACTIONf_chiral_restr0.056215
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5024-1.540.18711370.15921662X-RAY DIFFRACTION95
1.54-1.58160.1821410.16051726X-RAY DIFFRACTION96
1.5816-1.62810.17991410.15551725X-RAY DIFFRACTION96
1.6281-1.68070.1731400.1551705X-RAY DIFFRACTION97
1.6807-1.74080.21581430.16061736X-RAY DIFFRACTION96
1.7408-1.81040.20011420.16041724X-RAY DIFFRACTION97
1.8104-1.89280.19411420.16221731X-RAY DIFFRACTION97
1.8928-1.99260.16751440.15311759X-RAY DIFFRACTION97
1.9926-2.11750.1521420.14611733X-RAY DIFFRACTION98
2.1175-2.28090.1721450.15941775X-RAY DIFFRACTION98
2.2809-2.51040.1941450.1681760X-RAY DIFFRACTION98
2.5104-2.87350.18191430.16821751X-RAY DIFFRACTION99
2.8735-3.61970.16791490.15461796X-RAY DIFFRACTION99
3.6197-34.90160.17271460.15491791X-RAY DIFFRACTION98

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