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- PDB-4fq0: Crystal structure of FliG-FliM complex from H. pylori -

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Basic information

Entry
Database: PDB / ID: 4fq0
TitleCrystal structure of FliG-FliM complex from H. pylori
Components(Flagellar motor switch protein) x 2
KeywordsMOTOR PROTEIN / flagellar motor switch complex / FliG-FliM-FliN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG, alpha-alpha superhelical domain / CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliG / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain ...Flagellar motor switch protein FliG, alpha-alpha superhelical domain / CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliG / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / Flagellar motor switch protein FliM / FliG middle domain / FliG N-terminal domain / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / Annexin V; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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
DepositionJun 24, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,0774
Polymers72,0774
Non-polymers00
Water1629
1
B: Flagellar motor switch protein
C: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)36,0392
Polymers36,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area11890 Å2
MethodPISA
2
A: Flagellar motor switch protein
D: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)36,0392
Polymers36,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-5 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.085, 124.540, 137.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUBA51 - 22724 - 200
21GLUGLULEULEUAB51 - 22724 - 200
12LYSLYSGLUGLUCC117 - 19623 - 102
22LYSLYSGLUGLUDD117 - 19623 - 102

NCS ensembles :
ID
1
2

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Components

#1: Protein Flagellar motor switch protein / / FliM


Mass: 23550.412 Da / Num. of mol.: 2 / Fragment: UNP residues 33-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: FliM / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25675
#2: Protein Flagellar motor switch protein / / FliG


Mass: 12488.308 Da / Num. of mol.: 2 / Fragment: UNP residues 116-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: FliG / Plasmid: pAC28m / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25119
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.6M Ammonium sulfate, 0.2M Lithium sulfate, 0.1M CAPSO, 3%(v/v) Methanol, pH 10.5, VAPOR DIFFUSION, SITTING 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: Mar 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15973 / Redundancy: 5.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→36.77 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 47.165 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 4.948 / ESU R Free: 0.446
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30787 862 5.1 %RANDOM
Rwork0.23737 ---
obs0.24116 15973 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.158 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2---6.58 Å20 Å2
3---8.62 Å2
Refinement stepCycle: LAST / Resolution: 2.82→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 0 9 3974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194031
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9695471
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98525.346159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.3415702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3641516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212960
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B2090.22
12A2090.22
21C880.3
22D880.3
LS refinement shellResolution: 2.821→2.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.546 45 -
Rwork0.359 815 -
obs--71.19 %
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)
10.64550.2546-0.65492.829-0.81015.60030.07710.00390.10720.3567-0.19440.4102-0.0368-0.17110.11730.26550.01710.01550.2971-0.09880.2539-2.731913.3542-31.5139
20.5504-0.20320.54513.1996-0.48555.20160.07430.0074-0.0377-0.4047-0.22170.51380.0109-0.25930.14740.2684-0.0074-0.05110.283-0.12290.3658-2.6474-13.5816-35.4383
34.62883.261-1.33823.6206-0.30677.3802-0.1252-0.12630.409-0.00420.217-0.11260.28540.5919-0.09180.17280.0702-0.06680.3262-0.09330.173511.957316.2603-57.053
45.2229-2.76122.52095.70840.73058.9335-0.07580.0465-0.0632-0.12640.13730.0667-0.13950.5631-0.06160.1771-0.04270.07050.309-0.04470.033812.0722-16.3627-10.0825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B48 - 121
2X-RAY DIFFRACTION1B122 - 169
3X-RAY DIFFRACTION1B170 - 229
4X-RAY DIFFRACTION2A49 - 102
5X-RAY DIFFRACTION2A103 - 147
6X-RAY DIFFRACTION2A148 - 169
7X-RAY DIFFRACTION2A170 - 207
8X-RAY DIFFRACTION2A208 - 228
9X-RAY DIFFRACTION3C117 - 145
10X-RAY DIFFRACTION3C146 - 180
11X-RAY DIFFRACTION3C181 - 196
12X-RAY DIFFRACTION4D117 - 138
13X-RAY DIFFRACTION4D139 - 180
14X-RAY DIFFRACTION4D181 - 196

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