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- PDB-6ch2: Crystal structure of the cytoplasmic domain of FlhA and FliT-FliD... -

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Basic information

Entry
Database: PDB / ID: 6ch2
TitleCrystal structure of the cytoplasmic domain of FlhA and FliT-FliD complex
Components
  • Flagellar biosynthesis protein FlhA
  • Flagellar hook-associated protein 2,Flagellar protein FliT
KeywordsSTRUCTURAL PROTEIN / flagellar
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum organization / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / protein secretion / protein folding / cell adhesion / extracellular region ...negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum organization / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / protein secretion / protein folding / cell adhesion / extracellular region / plasma membrane / cytosol
Similarity search - Function
Flagellar protein FliT / Flagellar protein FliT / Flagellar hook-associated protein 2, N-terminal / Flagellar biosynthesis protein FlhA / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / FHIPEP family, domain 1 / Flagellin hook, IN motif ...Flagellar protein FliT / Flagellar protein FliT / Flagellar hook-associated protein 2, N-terminal / Flagellar biosynthesis protein FlhA / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / FHIPEP family, domain 1 / Flagellin hook, IN motif / Flagellin hook IN motif / 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 protein FliT / Flagellar hook-associated protein 2 / Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Salmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXing, Q. / Shi, K. / Kalodimos, C.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073854 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
B: Flagellar biosynthesis protein FlhA
C: Flagellar biosynthesis protein FlhA
D: Flagellar hook-associated protein 2,Flagellar protein FliT
E: Flagellar hook-associated protein 2,Flagellar protein FliT
F: Flagellar hook-associated protein 2,Flagellar protein FliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,0708
Polymers168,8866
Non-polymers1842
Water73941
1
A: Flagellar biosynthesis protein FlhA
D: Flagellar hook-associated protein 2,Flagellar protein FliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3873
Polymers56,2952
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar biosynthesis protein FlhA
E: Flagellar hook-associated protein 2,Flagellar protein FliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3873
Polymers56,2952
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Flagellar biosynthesis protein FlhA
F: Flagellar hook-associated protein 2,Flagellar protein FliT


Theoretical massNumber of molelcules
Total (without water)56,2952
Polymers56,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.110, 77.590, 119.270
Angle α, β, γ (deg.)86.88, 89.00, 84.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Flagellar biosynthesis protein FlhA


Mass: 36740.309 Da / Num. of mol.: 3 / 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: Protein Flagellar hook-associated protein 2,Flagellar protein FliT / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 19555.023 Da / Num. of mol.: 3 / Fragment: unp residues 1-122; 428-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria), (gene. exp.) Salmonella typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliD, flaV, flbC, STM1960, fliT, STY2170, t0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P16328, UniProt: P0A1N3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: CaCl2, PEG8000, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→39.695 Å / Num. obs: 44673 / % possible obs: 92.98 % / Redundancy: 2.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 9.16
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.62 / Rsym value: 0.74 / % possible all: 93.68

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A5I

3a5i


Resolution: 2.7→39.695 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1990 4.46 %
Rwork0.2334 --
obs0.2348 44667 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11161 0 12 41 11214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211337
X-RAY DIFFRACTIONf_angle_d0.54715354
X-RAY DIFFRACTIONf_dihedral_angle_d16.1614307
X-RAY DIFFRACTIONf_chiral_restr0.0571801
X-RAY DIFFRACTIONf_plane_restr0.0031996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.42031470.44223080X-RAY DIFFRACTION94
2.7675-2.84230.41741440.38833074X-RAY DIFFRACTION93
2.8423-2.92590.40341400.36263048X-RAY DIFFRACTION93
2.9259-3.02030.36951380.34933031X-RAY DIFFRACTION93
3.0203-3.12820.3751350.34112966X-RAY DIFFRACTION90
3.1282-3.25340.37951420.31353059X-RAY DIFFRACTION93
3.2534-3.40140.32171480.29523097X-RAY DIFFRACTION95
3.4014-3.58070.31061420.2613052X-RAY DIFFRACTION94
3.5807-3.80480.27811450.24223093X-RAY DIFFRACTION93
3.8048-4.09830.25271390.21982991X-RAY DIFFRACTION91
4.0983-4.51020.24821440.19053028X-RAY DIFFRACTION92
4.5102-5.16170.19111420.18363059X-RAY DIFFRACTION93
5.1617-6.49850.25981380.21492997X-RAY DIFFRACTION92
6.4985-39.69910.18461460.16013102X-RAY DIFFRACTION94
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)
10.1323-0.06770.08930.12580.02890.2819-0.03820.0204-0.4670.1866-0.08290.24530.2748-0.0092-0.01150.56940.058-0.10010.40230.1340.4891-3.9704-43.929-9.7376
20.3928-0.04220.33050.1513-0.11960.4173-0.06580.0823-0.12790.05880.1747-0.0298-0.11170.133-00.3996-0.04490.00320.5817-0.07940.389620.8008-25.6326-13.2602
3-0.01070.07450.03620.09520.02650.02780.1162-0.0610.3593-0.06480.118-0.185-0.08650.310100.6423-0.10410.06430.57650.00610.54675.0811-30.6504-51.0602
40.04520.0283-0.02920.0306-0.0030.045-0.0363-0.2330.3308-0.05230.23710.23590.0283-0.14280.00010.586-0.0016-0.04590.46810.09570.3801-1.3589-35.8891-46.3061
50.03550.0048-0.00480.0693-0.03520.01250.14140.05370.03780.1458-0.0938-0.0074-0.14770.427100.462-0.04920.05080.53330.00090.460213.2117-50.615-57.358
60.21520.027-0.1464-0.00360.05190.1939-0.0749-0.53190.2356-0.0717-0.01310.4119-0.54980.31670.0080.80210.0951-0.10950.2809-0.0930.7566-11.5962-26.6706-59.7483
70.0205-0.01290.00910.03660.04440.0395-0.338-0.15910.0240.0112-0.08950.2665-0.3172-0.067100.67070.0962-0.21930.50190.08830.7818-22.3812-28.2835-67.9661
80.026-0.06050.02630.0663-0.0287-0.007-0.01380.34670.1307-0.0404-0.0884-0.08710.1676-0.073300.50260.04330.10150.68730.00770.6986-19.6637-45.8792-77.8712
90.08570.00660.03010.10570.02330.07230.00490.5372-0.433-0.0201-0.1154-0.12870.1034-0.019600.45520.1225-0.0450.65160.09310.4837-16.0681-48.5824-74.245
100.05550.05630.01380.04510.03770.0359-0.25680.1473-0.09090.04250.15990.29940.05740.088800.7393-0.0265-0.04250.6313-0.06150.7796-1.753419.0011-29.3033
110.32190.20360.03840.0705-0.03240.1918-0.10790.1638-0.05190.1305-0.17480.16330.0521-0.2815-0.10960.5706-0.06480.13930.36290.02020.4938-6.69166.7933-32.8541
120.1557-0.18840.01340.16520.130.09960.1360.1109-0.1696-0.0513-0.32740.7051-0.10780.0802-0.00030.8421-0.08590.07110.4576-0.08150.7325-1.8478-13.6093-38.9147
130.0542-0.08740.09040.5877-0.48240.4056-0.0564-0.29270.4883-0.33080.0942-0.12570.1988-0.04750.040.4591-0.01550.10480.8324-0.35040.9619-2.2452-0.20018.9035
140.1417-0.12030.04660.1497-0.18780.64290.1813-0.76430.5501-0.00340.08160.02890.308-0.17120.60170.07050.05260.27790.6428-0.54070.8627-9.09613.004413.5991
150.26750.23080.00060.442-0.44620.8268-0.1211.0946-0.68840.05380.0180.1014-0.4001-0.1950.09710.0659-0.04180.06891.2812-0.68370.95768.7793-68.0679-97.9383
160.1161-0.0194-0.14990.56170.10340.42780.17430.4209-0.37640.16670.0136-0.1043-0.0791-0.0690.08290.35880.0143-0.03620.958-0.46770.93398.7149-67.0569-92.9665
17-0.00110.0087-0.01070.0072-0.00470.01080.07610.06250.1493-0.17270.00820.05760.19320.05920.00021.8940.06780.28661.0125-0.13011.2157-8.2295-9.8536-69.2267
18-0.0016-0.01040.01490.0097-0.01250.014-0.06520.0263-0.11680.0651-0.2451-0.05-0.00290.10601.9596-0.0403-0.06051.3565-0.14991.4437-7.2805-12.5061-89.2709
190.0066-0.0050.0213-0.00380.00720.0124-0.11940.0104-0.27110.066-0.0621-0.06480.10930.0317-01.6444-0.1586-0.08481.1081-0.03351.3497-9.7769-18.9046-87.2826
20-0.0325-0.02470.05770.1014-0.10840.07910.30830.62790.1145-0.061-0.33120.09690.070.415501.08390.2059-0.13611.1642-0.14160.6922-2.647-3.4763-69.0449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 360 through 498 )
2X-RAY DIFFRACTION2chain 'A' and (resid 499 through 690 )
3X-RAY DIFFRACTION3chain 'B' and (resid 359 through 397 )
4X-RAY DIFFRACTION4chain 'B' and (resid 398 through 431 )
5X-RAY DIFFRACTION5chain 'B' and (resid 432 through 479 )
6X-RAY DIFFRACTION6chain 'B' and (resid 480 through 533 )
7X-RAY DIFFRACTION7chain 'B' and (resid 534 through 581 )
8X-RAY DIFFRACTION8chain 'B' and (resid 582 through 621 )
9X-RAY DIFFRACTION9chain 'B' and (resid 622 through 690 )
10X-RAY DIFFRACTION10chain 'C' and (resid 360 through 431 )
11X-RAY DIFFRACTION11chain 'C' and (resid 432 through 564 )
12X-RAY DIFFRACTION12chain 'C' and (resid 565 through 690 )
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 41 )
14X-RAY DIFFRACTION14chain 'D' and (resid 42 through 164 )
15X-RAY DIFFRACTION15chain 'E' and (resid 4 through 83 )
16X-RAY DIFFRACTION16chain 'E' and (resid 84 through 165 )
17X-RAY DIFFRACTION17chain 'F' and (resid 4 through 35 )
18X-RAY DIFFRACTION18chain 'F' and (resid 36 through 86 )
19X-RAY DIFFRACTION19chain 'F' and (resid 87 through 117 )
20X-RAY DIFFRACTION20chain 'F' and (resid 118 through 173 )

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