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- PDB-6ch1: Crystal structure of the cytoplasmic domain of FlhA in monomeric form -

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Basic information

Entry
Database: PDB / ID: 6ch1
TitleCrystal structure of the cytoplasmic domain of FlhA in monomeric form
ComponentsFlagellar biosynthesis protein FlhA
KeywordsSTRUCTURAL PROTEIN / flagellar
Function / homology
Function and homology information


bacterial-type flagellum assembly / protein secretion / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin ...Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXing, Q. / Shi, K. / Kalodimos, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2018
Title: Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system.
Authors: Xing, Q. / Shi, K. / Portaliou, A. / Rossi, P. / Economou, A. / Kalodimos, C.G.
History
DepositionFeb 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 biosynthesis protein FlhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,54110
Polymers36,9831
Non-polymers5599
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.380, 49.970, 50.950
Angle α, β, γ (deg.)78.04, 68.99, 80.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Flagellar biosynthesis protein FlhA


Mass: 36982.547 Da / Num. of mol.: 1 / Fragment: UNP residues 360-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: flhA, STM1913 / Production host: Escherichia coli (E. coli) / References: UniProt: P40729
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: tri-ammonium citrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→193 Å / Num. obs: 27461 / % possible obs: 96.2 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1391 / CC1/2: 0.54 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(DEV_2706: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A5I

3a5i


Resolution: 1.9→19.92 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 1297 4.73 %
Rwork0.198 --
obs0.2 27439 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 36 211 2815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042662
X-RAY DIFFRACTIONf_angle_d0.6043598
X-RAY DIFFRACTIONf_dihedral_angle_d19.8191008
X-RAY DIFFRACTIONf_chiral_restr0.057418
X-RAY DIFFRACTIONf_plane_restr0.003471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.3491580.31942871X-RAY DIFFRACTION95
1.9761-2.06590.26441410.26132888X-RAY DIFFRACTION96
2.0659-2.17470.26211590.22432911X-RAY DIFFRACTION96
2.1747-2.31080.26971420.20552907X-RAY DIFFRACTION96
2.3108-2.48890.23511260.19892918X-RAY DIFFRACTION96
2.4889-2.73880.27421390.19862902X-RAY DIFFRACTION97
2.7388-3.13370.24371380.20032954X-RAY DIFFRACTION96
3.1337-3.94320.22511540.1862894X-RAY DIFFRACTION97
3.9432-19.91570.20431400.17732897X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -28.5622 Å / Origin y: -6.1147 Å / Origin z: -22.7666 Å
111213212223313233
T0.1735 Å2-0.0187 Å20.005 Å2-0.2389 Å20.0132 Å2--0.1957 Å2
L1.0433 °20.0561 °20.1689 °2-1.2761 °20.1144 °2--0.884 °2
S0.0583 Å °0.0172 Å °0.014 Å °0.031 Å °-0.0236 Å °0.0584 Å °0.0312 Å °0.0123 Å °-0.0328 Å °
Refinement TLS groupSelection details: ALL

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