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- PDB-4rz2: Crystal structure of the MinD-like ATPase FlhG -

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Basic information

Entry
Database: PDB / ID: 4rz2
TitleCrystal structure of the MinD-like ATPase FlhG
ComponentsSite-determining protein
KeywordsSTRUCTURAL PROTEIN / P-loop / Walker A / SIMIBI / flagellum / cell division
Function / homology
Function and homology information


negative regulation of cell division / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Flagellum site-determining protein FlhG / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / : / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar synthesis regulator fleN
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchuhmacher, J.S. / Bange, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: MinD-like ATPase FlhG effects location and number of bacterial flagella during C-ring assembly.
Authors: Schuhmacher, J.S. / Rossmann, F. / Dempwolff, F. / Knauer, C. / Altegoer, F. / Steinchen, W. / Dorrich, A.K. / Klingl, A. / Stephan, M. / Linne, U. / Thormann, K.M. / Bange, G.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 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 / 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: Site-determining protein
B: Site-determining protein


Theoretical massNumber of molelcules
Total (without water)65,3212
Polymers65,3212
Non-polymers00
Water1,02757
1
A: Site-determining protein


Theoretical massNumber of molelcules
Total (without water)32,6601
Polymers32,6601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Site-determining protein


Theoretical massNumber of molelcules
Total (without water)32,6601
Polymers32,6601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.870, 89.360, 111.880
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 Site-determining protein


Mass: 32660.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80, NG80-2 / Gene: GTNG_1094 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A4IMB4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 10 % (w/v) PEG 8000, 0.1 M Urea, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→51.96 Å / Num. obs: 16375 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QL9

3ql9


Resolution: 2.8→47.416 Å / SU ML: 0.31 / σ(F): 0.03 / Phase error: 21.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1592 10 %RANDOM
Rwork0.1772 ---
obs0.1824 15916 97.45 %-
all-0 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 0 57 4003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084031
X-RAY DIFFRACTIONf_angle_d1.2285449
X-RAY DIFFRACTIONf_dihedral_angle_d13.8731472
X-RAY DIFFRACTIONf_chiral_restr0.084616
X-RAY DIFFRACTIONf_plane_restr0.005697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.31311340.24631211X-RAY DIFFRACTION93
2.8904-2.99370.26061390.20511251X-RAY DIFFRACTION96
2.9937-3.11360.241410.20681256X-RAY DIFFRACTION96
3.1136-3.25520.27881390.20191265X-RAY DIFFRACTION96
3.2552-3.42680.26481440.20131292X-RAY DIFFRACTION98
3.4268-3.64140.22981440.17931296X-RAY DIFFRACTION98
3.6414-3.92250.24061460.16321320X-RAY DIFFRACTION99
3.9225-4.3170.21291480.15391320X-RAY DIFFRACTION99
4.317-4.94110.1841470.14431330X-RAY DIFFRACTION99
4.9411-6.2230.20041510.15971351X-RAY DIFFRACTION99
6.223-47.42230.20221590.17421432X-RAY DIFFRACTION99

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