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- PDB-4gc8: Crystal structure of FliM middle domain from H. pylori -

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Basic information

Entry
Database: PDB / ID: 4gc8
TitleCrystal structure of FliM middle domain from H. pylori
ComponentsFlagellar motor switch protein
KeywordsMOTOR PROTEIN / Flagellar motor switch / chemotaxis / flagellation / FliN / FliG / CheY
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / plasma membrane
Similarity search - Function
CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLam, K.H. / Au, S.W.N.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structural basis of FliG-FliM interaction in Helicobacter pylori
Authors: Lam, K.H. / Lam, W.W.L. / Wong, J.Y. / Chan, L.C. / Kotaka, M. / Ling, T.K.W. / Jin, D.Y. / Ottemann, K.M. / Au, S.W.N.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar motor switch protein
B: Flagellar motor switch protein
C: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)71,3303
Polymers71,3303
Non-polymers00
Water3,009167
1
A: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.267, 91.267, 57.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Flagellar motor switch protein / FliM


Mass: 23776.727 Da / Num. of mol.: 3 / Fragment: residues 31-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: FliM / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O25675
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG2250, 20mM Sodium Bromide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 26406 / Biso Wilson estimate: 30.84 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.846 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8236 / SU ML: 0.3 / σ(F): 2.04 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1335 5.06 %
Rwork0.1755 --
obs0.1787 26406 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.08 Å2 / Biso mean: 36.1242 Å2 / Biso min: 11.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 0 167 4307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084202
X-RAY DIFFRACTIONf_angle_d1.1175670
X-RAY DIFFRACTIONf_chiral_restr0.072679
X-RAY DIFFRACTIONf_plane_restr0.006714
X-RAY DIFFRACTIONf_dihedral_angle_d15.0791601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27860.32311280.22962493262197
2.2786-2.36980.32331130.21422506261998
2.3698-2.47760.26191150.20222543265898
2.4776-2.60810.28811600.19972477263798
2.6081-2.77140.29381270.20872538266599
2.7714-2.98510.2931360.20042538267499
2.9851-3.2850.2431440.1922523266799
3.285-3.75930.26941480.16872526267499
3.7593-4.73210.17221410.13232523266499
4.7321-26.84820.17561230.15372404252794
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)
13.7312-1.49030.29848.0425-5.95167.64950.09450.4608-0.2117-0.55410.13050.87460.7705-0.1388-0.25240.2612-0.007-0.04490.3461-0.08380.316425.8776-34.5588-24.919
23.05680.6125-0.81363.1048-0.89584.2991-0.11550.08670.13160.05680.25060.27480.1016-0.1825-0.1440.13310.0159-0.00140.21660.03420.170329.613-23.6876-19.3343
33.9352-1.0558-0.05672.9669-0.82165.958-0.2551-0.4868-0.02430.32170.15370.08930.49690.26440.12130.13960.0087-0.00190.22080.01190.202335.0438-30.941-12.4981
42.88470.1628-1.43213.1667-0.60614.4394-0.0146-0.0380.17290.05760.13040.1444-0.14930.0493-0.12540.11220.0374-0.0130.21310.01610.177431.1334-22.6662-21.4705
53.5421.24061.40077.08365.91949.8410.05230.2447-0.00370.1564-0.3383-0.4033-0.31340.41980.2910.26060.0015-0.0170.22380.10330.356121.2038-1.012-48.5409
62.63490.10390.47122.4616-0.94613.4270.2930.0229-0.49670.2574-0.035-0.22290.26680.1475-0.2270.30090.0094-0.04440.13880.0010.34513.322-9.0223-43.0726
72.3325-0.9634-0.93181.79410.82296.6158-0.0881-0.0764-0.07720.21250.0484-0.1891-0.4819-0.16870.01750.1812-0.0107-0.02310.11990.02070.241311.2966-0.5476-36.3207
83.0286-0.74711.2441.44150.34214.657-0.02660.2013-0.23250.12150.00390.05870.11-0.1211-0.00060.2385-0.0032-0.01620.11320.04430.314811.3133-9.5551-45.2737
92.44080.2269-0.45772.7819-0.83523.16780.1648-0.20250.25210.1795-0.0207-0.0738-0.44190.1068-0.13880.2184-0.00420.04810.1376-0.03280.2328-0.2141-35.4419-45.1372
103.0904-1.34712.22112.504-0.91566.85020.23760.37130.0869-0.3102-0.2805-0.0879-0.07290.43140.09330.2128-0.01250.06030.1597-0.00850.28591.2689-41.4775-55.2777
112.65190.8413-1.00674.3693-2.62624.86540.1351-0.0252-0.04270.05260.10190.163-0.0732-0.1852-0.32960.1860.02810.03650.1569-0.00440.244-5.5429-37.4672-43.7586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain C and (resid 48 through 75 )C0
2X-RAY DIFFRACTION2chain C and (resid 76 through 121 )C0
3X-RAY DIFFRACTION3chain C and (resid 122 through 177 )C0
4X-RAY DIFFRACTION4chain C and (resid 178 through 230 )C0
5X-RAY DIFFRACTION5chain B and (resid 48 through 75 )B0
6X-RAY DIFFRACTION6chain B and (resid 76 through 121 )B0
7X-RAY DIFFRACTION7chain B and (resid 122 through 177 )B0
8X-RAY DIFFRACTION8chain B and (resid 178 through 230 )B0
9X-RAY DIFFRACTION9chain A and (resid 47 through 121 )A0
10X-RAY DIFFRACTION10chain A and (resid 122 through 183 )A0
11X-RAY DIFFRACTION11chain A and (resid 184 through 230 )A0

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