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- PDB-6ch3: Crystal structure of the cytoplasmic domain of FlhA and FliS-FliC... -

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Basic information

Entry
Database: PDB / ID: 6ch3
TitleCrystal structure of the cytoplasmic domain of FlhA and FliS-FliC complex
Components
  • Flagellar biosynthesis protein FlhA
  • Flagellar secretion chaperone FliS,Flagellin
KeywordsSTRUCTURAL PROTEIN / flagellar
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / protein secretion / structural molecule activity / extracellular region ...TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / protein secretion / structural molecule activity / extracellular region / plasma membrane / cytosol
Similarity search - Function
: / Flagellin, barrel domain / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / Flagellin D3 / Flagellin D3 domain / FHIPEP, domain 1 ...: / Flagellin, barrel domain / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / Flagellin D3 / Flagellin D3 domain / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellin / Flagellar secretion chaperone FliS / Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 1.1Sep 18, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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

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Assembly

Deposited unit
A: Flagellar biosynthesis protein FlhA
B: Flagellar secretion chaperone FliS,Flagellin


Theoretical massNumber of molelcules
Total (without water)57,4222
Polymers57,4222
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-16 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.298, 88.623, 117.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flagellar biosynthesis protein FlhA


Mass: 36497.027 Da / Num. of mol.: 1
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: Protein Flagellar secretion chaperone FliS,Flagellin / Phase 1-A flagellin / Phase 1-I flagellin


Mass: 20925.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria), (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliS, STM1961, fliS, t0916, fliC, flaF, hag, STM1959 / Production host: Escherichia coli (E. coli) / References: UniProt: P26609, UniProt: P06179
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: tascimate

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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: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→35 Å / Num. obs: 21804 / % possible obs: 98.69 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.045 / Rrim(I) all: 0.106 / Rsym value: 0.096 / Net I/σ(I): 15.7
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.13 / Num. unique obs: 7894 / CC1/2: 0.512 / Rpim(I) all: 0.636 / Rrim(I) all: 1.3 / % possible all: 91.74

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→34.982 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1119 5.13 %
Rwork0.2332 --
obs0.2345 21804 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→34.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 0 6 3765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023811
X-RAY DIFFRACTIONf_angle_d0.4585163
X-RAY DIFFRACTIONf_dihedral_angle_d12.1322348
X-RAY DIFFRACTIONf_chiral_restr0.037609
X-RAY DIFFRACTIONf_plane_restr0.004676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.8020.3791390.37792371X-RAY DIFFRACTION93
2.802-2.94960.42221190.33972566X-RAY DIFFRACTION98
2.9496-3.13430.35011460.30312548X-RAY DIFFRACTION100
3.1343-3.37610.3311400.27952596X-RAY DIFFRACTION100
3.3761-3.71550.2551250.24782610X-RAY DIFFRACTION100
3.7155-4.25240.23621280.2092632X-RAY DIFFRACTION100
4.2524-5.35450.21961420.18852651X-RAY DIFFRACTION100
5.3545-34.9850.21231800.1992711X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3090.9317-1.78331.9307-0.92724.2152-0.0193-0.01290.10220.05690.0184-0.0078-0.0654-0.48620.01240.43060.0726-0.05460.4283-0.05980.437-14.007943.3184.96
22.52650.38840.2183.85391.94655.68740.08480.05370.175-0.21340.0624-0.4123-0.70960.5247-0.00580.7681-0.04510.10120.68520.01470.4781-14.216147.159534.4173
32.427-0.8338-2.15758.41151.60342.0784-0.174-0.2143-0.00570.2947-0.06390.04720.05810.20840.22350.45650.065-0.10750.5218-0.03410.5188-4.926737.61858.1159
42.735-0.334-0.30783.50270.64611.499-0.0450.03810.30870.10430.154-0.2123-0.06660.08320.05510.33960.0137-0.00980.5777-0.03960.43639.976232.07470.4629
55.86760.80090.63233.76950.56741.71460.07390.3057-0.0083-0.11260.052-0.0044-0.0302-0.0802-0.03930.36140.03810.04920.6454-0.05420.339613.487523.9131-5.5459
62.40431.15491.81374.9733-0.57842.1250.625-0.3615-0.2996-0.2851-0.66180.4876-0.4652-0.94370.07680.53890.0432-0.04720.8885-0.18550.41825.532419.0143-13.0223
76.14061.7531.03799.29162.74484.29070.0159-0.089-0.20320.69940.26630.18730.4525-0.2318-0.34720.35940.0195-0.05060.70250.04470.38290.081121.98973.5288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 360 through 519 )
2X-RAY DIFFRACTION2chain 'A' and (resid 520 through 690 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 23 )
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 74 )
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 123 )
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 176 )
7X-RAY DIFFRACTION7chain 'B' and (resid 177 through 198 )

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