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- PDB-4qrm: crystal structure of a binary complex of FliM-FliG middle domains... -

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Basic information

Entry
Database: PDB / ID: 4qrm
Titlecrystal structure of a binary complex of FliM-FliG middle domains from T.maritima
Components
  • Flagellar motor switch protein FliGFlagellar motor switch protein
  • Flagellar motor switch protein FliMFlagellar motor switch protein
KeywordsPROTEIN BINDING / Flagellar rotor proteins
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / protein heterodimerization activity / protein homodimerization activity / plasma membrane
Similarity search - Function
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 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
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.315 Å
AuthorsCrane, B.R. / Sircar, R.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Assembly states of FliM and FliG within the flagellar switch complex.
Authors: Sircar, R. / Borbat, P.P. / Lynch, M.J. / Bhatnagar, J. / Beyersdorf, M.S. / Halkides, C.J. / Freed, J.H. / Crane, B.R.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

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Assembly

Deposited unit
A: Flagellar motor switch protein FliM
B: Flagellar motor switch protein FliG
C: Flagellar motor switch protein FliM
D: Flagellar motor switch protein FliG
E: Flagellar motor switch protein FliM
F: Flagellar motor switch protein FliG
G: Flagellar motor switch protein FliM
H: Flagellar motor switch protein FliG
I: Flagellar motor switch protein FliM
J: Flagellar motor switch protein FliG
K: Flagellar motor switch protein FliM
L: Flagellar motor switch protein FliG
M: Flagellar motor switch protein FliM
N: Flagellar motor switch protein FliG
O: Flagellar motor switch protein FliM
P: Flagellar motor switch protein FliG
Q: Flagellar motor switch protein FliM
R: Flagellar motor switch protein FliG
S: Flagellar motor switch protein FliM
T: Flagellar motor switch protein FliG
U: Flagellar motor switch protein FliM
V: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)323,75022
Polymers323,75022
Non-polymers00
Water0
1
A: Flagellar motor switch protein FliM
B: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Flagellar motor switch protein FliM
D: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Flagellar motor switch protein FliM
F: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Flagellar motor switch protein FliM
H: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Flagellar motor switch protein FliM
J: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
Q: Flagellar motor switch protein FliM
R: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Flagellar motor switch protein FliM
T: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
U: Flagellar motor switch protein FliM
V: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
K: Flagellar motor switch protein FliM
L: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
M: Flagellar motor switch protein FliM
N: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
O: Flagellar motor switch protein FliM
P: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)29,4322
Polymers29,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.403, 216.255, 262.214
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 motor switch protein FliM / Flagellar motor switch protein


Mass: 21060.180 Da / Num. of mol.: 11
Fragment: Middle domain, Chain A, C, E, G, I, K, M, O, Q, S, U
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: fliM, TM_0679, ThemaDRAFT_0623 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZE6
#2: Protein
Flagellar motor switch protein FliG / Flagellar motor switch protein


Mass: 8371.676 Da / Num. of mol.: 11
Fragment: Middle domain, Chain B, D, F, H, J, L, N, P, R, T, V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: fliG, TM_0220 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WY63

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, pH 6.5, 1.2 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: 2012 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. all: 37362 / Num. obs: 36914 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.315→44.18 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2908 1807 4.9 %Random
Rwork0.2087 ---
obs0.2128 36914 89.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.315→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22777 0 0 0 22777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523294
X-RAY DIFFRACTIONf_angle_d0.86631664
X-RAY DIFFRACTIONf_dihedral_angle_d15.1968678
X-RAY DIFFRACTIONf_chiral_restr0.0323685
X-RAY DIFFRACTIONf_plane_restr0.0054047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.315-4.43150.35411160.2722281X-RAY DIFFRACTION77
4.4315-4.56180.36671290.23872497X-RAY DIFFRACTION84
4.5618-4.70890.28091320.21912445X-RAY DIFFRACTION83
4.7089-4.8770.36341330.23592538X-RAY DIFFRACTION86
4.877-5.0720.26621250.22812589X-RAY DIFFRACTION87
5.072-5.30240.31591410.22962677X-RAY DIFFRACTION90
5.3024-5.58150.34091380.24222668X-RAY DIFFRACTION89
5.5815-5.93040.36391390.25052701X-RAY DIFFRACTION91
5.9304-6.38710.30741420.26182768X-RAY DIFFRACTION92
6.3871-7.02750.33531480.22952894X-RAY DIFFRACTION95
7.0275-8.03910.32731510.20152929X-RAY DIFFRACTION97
8.0391-10.10840.18991560.15463032X-RAY DIFFRACTION99
10.1084-44.18250.25861570.17133088X-RAY DIFFRACTION96

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