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- PDB-6ndx: Lysinoalanine cross-linked FlgE dimer from Treponema denticola -

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Basic information

Entry
Database: PDB / ID: 6ndx
TitleLysinoalanine cross-linked FlgE dimer from Treponema denticola
Components(Flagellar hook protein FlgE) x 2
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 / MOLECULAR REPLACEMENT / Resolution: 3.04 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.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 1.4Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Flagellar hook protein FlgE
A: Flagellar hook protein FlgE
C: Flagellar hook protein FlgE
D: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)108,9834
Polymers108,9834
Non-polymers00
Water905
1
B: Flagellar hook protein FlgE
D: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)54,4912
Polymers54,4912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Flagellar hook protein FlgE
C: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)54,4912
Polymers54,4912
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.565, 136.352, 112.184
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagellar hook protein FlgE


Mass: 35533.832 Da / Num. of mol.: 2 / Mutation: C178A
Source method: isolated from a genetically manipulated source
Details: FlgE(N91-S423) degraded prior to crystallization, N and C termini are missing from structure
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: flgE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RQB6
#2: Protein Flagellar hook protein FlgE


Mass: 18957.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 4 residues on C-termini missing from density, D-alanine present instead of cysteine
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: flgE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RQB6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: crystallized in two conditions: (1) 100 mM Tris pH 8.5, 20% (w/v) PEG8000, 200 mM magnesium chloride and (2) 200 mM magnesium acetate, 20% PEG3350 (w/v)

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.04→43.1 Å / Num. obs: 28592 / % possible obs: 96.7 % / Redundancy: 4.1 % / Net I/σ(I): 7.7
Reflection shellResolution: 3.04→3.13 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→43.1 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.82
RfactorNum. reflection% reflection
Rfree0.3157 1849 6.97 %
Rwork0.2477 --
obs0.2525 26528 89.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.04→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 0 5 5774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135871
X-RAY DIFFRACTIONf_angle_d1.5678011
X-RAY DIFFRACTIONf_dihedral_angle_d9.1793456
X-RAY DIFFRACTIONf_chiral_restr0.071924
X-RAY DIFFRACTIONf_plane_restr0.0111076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0915-3.2020.40891410.331853X-RAY DIFFRACTION86
3.202-3.33010.3621390.2931885X-RAY DIFFRACTION91
3.3301-3.48160.31851590.27112020X-RAY DIFFRACTION94
3.4816-3.66510.31181530.26641971X-RAY DIFFRACTION96
3.6651-3.89460.32441500.24172055X-RAY DIFFRACTION97
3.8946-4.1950.32331510.22532087X-RAY DIFFRACTION97
4.195-4.61680.27571560.20531968X-RAY DIFFRACTION93
4.6168-5.28380.28521550.19752080X-RAY DIFFRACTION99
5.2838-6.65310.31181560.25372087X-RAY DIFFRACTION99
6.6531-43.10.27881600.22242053X-RAY DIFFRACTION95

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