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- PDB-5tug: Archaellum periplasmic stator protein complex FlaF and FlaG from ... -

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Basic information

Entry
Database: PDB / ID: 5tug
TitleArchaellum periplasmic stator protein complex FlaF and FlaG from Sulfolobus acidocaldarius
Components(Flagellar biosynthesis protein ...) x 2
KeywordsMOTOR PROTEIN / beta-sandwich fold Archaellum assembly subunit Stator protein
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / identical protein binding / membrane
Similarity search - Function
: / Conserved flagellar protein F, immunoglobulin-like domain / Flagellin, archaea / Archaeal-type flagellin
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Flagellar biosynthesis protein FlaG / Flagellar protein F / Flagellar protein FlaG / Conserved flagellar protein F
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 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 1.1Jan 17, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Jun 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 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar biosynthesis protein FlaG
B: Flagellar biosynthesis protein FlaF
C: Flagellar biosynthesis protein FlaG
D: Flagellar biosynthesis protein FlaF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,28616
Polymers62,3814
Non-polymers90512
Water3,315184
1
A: Flagellar biosynthesis protein FlaG
B: Flagellar biosynthesis protein FlaF
hetero molecules

C: Flagellar biosynthesis protein FlaG
hetero molecules

D: Flagellar biosynthesis protein FlaF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,28616
Polymers62,3814
Non-polymers90512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_444y-1,-x+y-1,z-1/61
crystal symmetry operation6_555x-y,x,z+1/61
Buried area9790 Å2
ΔGint-12 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.919, 119.919, 152.403
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Flagellar biosynthesis protein ... , 2 types, 4 molecules ACBD

#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 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: A0A0U2VTR0, UniProt: Q4J9K7*PLUS
#2: Protein Flagellar biosynthesis protein FlaF


Mass: 16248.860 Da / Num. of mol.: 2 / Fragment: UNP residues 35-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_00615, ATZ20_03660 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: A0A0U3GEN4, UniProt: Q4J9K8*PLUS

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Non-polymers , 4 types, 196 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 5.07 Å3/Da / Density % sol: 75.74 % / Description: hexagonal
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG 6000 0.1M Tris, pH 7.5, 0.2M NaBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2015
RadiationMonochromator: ML crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.24
ReflectionResolution: 2.47→49.152 Å / Num. obs: 44562 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.2
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.291 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.774 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.25data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P94

4p94


Resolution: 2.47→49.152 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1935 2081 4.68 %
Rwork0.1634 --
obs0.1653 44511 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.47→49.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 61 184 4081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083985
X-RAY DIFFRACTIONf_angle_d0.9855451
X-RAY DIFFRACTIONf_dihedral_angle_d15.22324
X-RAY DIFFRACTIONf_chiral_restr0.06636
X-RAY DIFFRACTIONf_plane_restr0.008690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4709-2.52830.3371260.28242816X-RAY DIFFRACTION96
2.5283-2.59150.27681260.2752827X-RAY DIFFRACTION96
2.5915-2.66160.33891260.26422853X-RAY DIFFRACTION96
2.6616-2.73990.27631450.24272790X-RAY DIFFRACTION95
2.7399-2.82830.23031360.23482800X-RAY DIFFRACTION95
2.8283-2.92940.28161480.22032843X-RAY DIFFRACTION95
2.9294-3.04660.29141500.21072763X-RAY DIFFRACTION95
3.0466-3.18520.21811260.18822865X-RAY DIFFRACTION96
3.1852-3.3530.21781550.17452801X-RAY DIFFRACTION95
3.353-3.5630.20321590.15842773X-RAY DIFFRACTION95
3.563-3.83790.17761430.15052843X-RAY DIFFRACTION95
3.8379-4.22360.15391210.1352842X-RAY DIFFRACTION96
4.2236-4.83380.13361490.11862829X-RAY DIFFRACTION95
4.8338-6.08630.14931280.12942841X-RAY DIFFRACTION96
6.0863-38.76450.16481430.1492871X-RAY DIFFRACTION95

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