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- PDB-8r9r: GDP-bound state of S. putrefaciens FlhF -

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Basic information

Entry
Database: PDB / ID: 8r9r
TitleGDP-bound state of S. putrefaciens FlhF
ComponentsFlagellar biosynthesis protein FlhF
KeywordsSIGNALING PROTEIN / Flagellum / Assembly / motility / GTP-binding / GTPase
Function / homology
Function and homology information


bacterial-type flagellum organization / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhF / : / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Flagellar biosynthesis protein FlhF
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMais, C.N. / Dornes, A. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)495924434 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Structure of the GDP-bound state of the SRP GTPase FlhF.
Authors: Dornes, A. / Mais, C.N. / Bange, G.
History
DepositionNov 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar biosynthesis protein FlhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7322
Polymers32,2891
Non-polymers4431
Water181
1
A: Flagellar biosynthesis protein FlhF
hetero molecules

A: Flagellar biosynthesis protein FlhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4644
Polymers64,5782
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)73.920, 73.920, 159.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Flagellar biosynthesis protein FlhF


Mass: 32288.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Gene: Sputcn32_2561 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y8J9
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1 M lithium chloride, 0.1 M citric acid, 20% PEG 6000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.42→40.97 Å / Num. obs: 100474 / % possible obs: 99.84 % / Redundancy: 35.8 % / CC1/2: 1 / Rmerge(I) obs: 0.1142 / Rpim(I) all: 0.01971 / Rrim(I) all: 0.116 / Net I/σ(I): 21.75
Reflection shellResolution: 2.42→2.507 Å / Rmerge(I) obs: 2.228 / Num. unique obs: 1001 / CC1/2: 0.754 / Rpim(I) all: 0.3613 / Rrim(I) all: 2.258

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→40.97 Å / SU B: 18.967 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.274 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25034 524 5 %RANDOM
Rwork0.2062 ---
obs0.20844 9955 99.81 %-
Displacement parametersBiso mean: 55 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å2-0 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.42→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 28 0 1 1965

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