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- PDB-5tuh: Archaellum periplasmic stator protein FlaG from Sulfolobus acidoc... -

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Basic information

Entry
Database: PDB / ID: 5tuh
TitleArchaellum periplasmic stator protein FlaG from Sulfolobus acidocaldarius
ComponentsFlagellar biosynthesis protein FlaG
KeywordsMOTOR PROTEIN / beta-sandwich fold Archaellum assembly subunit Stator protein Motor Protein / MEMBRANE PROTEIN
Function / homologyFlagellin, archaea / Archaeal-type flagellin / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellar biosynthesis protein FlaG / Flagellar protein FlaG
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.929 Å
AuthorsTsai, C.-L. / Tainer, J.A.
CitationJournal: Nat Microbiol / Year: 2020
Title: The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility.
Authors: Tsai, C.L. / Tripp, P. / Sivabalasarma, S. / Zhang, C. / Rodriguez-Franco, M. / Wipfler, R.L. / Chaudhury, P. / Banerjee, A. / Beeby, M. / Whitaker, R.J. / Tainer, J.A. / Albers, S.V.
History
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar biosynthesis protein FlaG
B: Flagellar biosynthesis protein FlaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9753
Polymers29,8832
Non-polymers921
Water2,432135
1
A: Flagellar biosynthesis protein FlaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0342
Polymers14,9411
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar biosynthesis protein FlaG


Theoretical massNumber of molelcules
Total (without water)14,9411
Polymers14,9411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.023, 100.316, 62.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Flagellar biosynthesis protein FlaG


Mass: 14941.408 Da / Num. of mol.: 2 / Fragment: UNP residues 32-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_00610, ATZ20_03655 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2VTR0, UniProt: Q4J9K7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.19 Å3/Da / Density % sol: 43.79 % / Description: needle
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 13%PEG3350, 0.2M sodium malonate, pH5, 3% 1,4 dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0714, 1.0448, 1.0718
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2015
RadiationMonochromator: ML crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07141
21.04481
31.07181
ReflectionResolution: 1.929→44.816 Å / Num. obs: 20112 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.93-1.9770.9762.10.724199.6
9.05-44.826.10.0320.999198.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
PHENIX(1.10_2155: ???)refinement
Aimless0.5.8data scaling
SOLVEphasing
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.929→44.816 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 989 4.92 %
Rwork0.1806 --
obs0.1822 20093 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.929→44.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 6 135 1775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071693
X-RAY DIFFRACTIONf_angle_d0.8152330
X-RAY DIFFRACTIONf_dihedral_angle_d11.422987
X-RAY DIFFRACTIONf_chiral_restr0.064273
X-RAY DIFFRACTIONf_plane_restr0.006294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9295-2.03120.2881340.24242685X-RAY DIFFRACTION100
2.0312-2.15850.26271310.20582704X-RAY DIFFRACTION100
2.1585-2.32510.22781400.18822703X-RAY DIFFRACTION100
2.3251-2.55910.23791460.18652675X-RAY DIFFRACTION100
2.5591-2.92930.20131450.19412726X-RAY DIFFRACTION100
2.9293-3.69040.22811410.17812763X-RAY DIFFRACTION100
3.6904-44.82850.18271520.16052848X-RAY DIFFRACTION100

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