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- PDB-6pbk: Archaellum periplasmic stator protein complex FlaF and FlaG from ... -

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Basic information

Entry
Database: PDB / ID: 6pbk
TitleArchaellum periplasmic stator protein complex FlaF and FlaG from Sulfolobus acidocaldarius
Components
  • Conserved flagellar protein F
  • Saci FlaG soluble domain
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 protein FlaG / Conserved flagellar protein F
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.805 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
DepositionJun 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
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 11, 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: Saci FlaG soluble domain
B: Conserved flagellar protein F
C: Saci FlaG soluble domain
D: Conserved flagellar protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,47818
Polymers62,4414
Non-polymers1,03714
Water2,648147
1
A: Saci FlaG soluble domain
B: Conserved flagellar protein F
hetero molecules

D: Conserved flagellar protein F
hetero molecules

C: Saci FlaG soluble domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,47818
Polymers62,4414
Non-polymers1,03714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation6_565x-y,x+1,z+1/61
Buried area10700 Å2
ΔGint-42 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.038, 120.038, 152.138
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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Protein , 2 types, 4 molecules ACBD

#1: Protein Saci FlaG soluble domain


Mass: 14971.457 Da / Num. of mol.: 2 / Mutation: V118K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_1176 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9K7
#2: Protein Conserved flagellar protein F


Mass: 16248.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_1175 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9K8

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Non-polymers , 5 types, 161 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 75.73 % / Description: hexagonal bi-pyramidal
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG 6000, 0.1 M Tris, pH 7.5, and 0.2 M NaBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→49.19 Å / Num. obs: 30449 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 77.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.034 / Rrim(I) all: 0.09 / Net I/σ(I): 16.4 / Num. measured all: 206623
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.966.81.2653001744090.6820.5211.371.599.7
8.87-49.196.50.025644599210.010.02756.399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.09 Å49.19 Å
Translation7.09 Å49.19 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.5.27data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P94, 5TUH

4p94

5tuh


Resolution: 2.805→39.292 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1542 5.08 %
Rwork0.1713 --
obs0.1728 30378 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.805→39.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 68 147 4055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094015
X-RAY DIFFRACTIONf_angle_d1.0975491
X-RAY DIFFRACTIONf_dihedral_angle_d4.2022744
X-RAY DIFFRACTIONf_chiral_restr0.066636
X-RAY DIFFRACTIONf_plane_restr0.007693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.805-2.89550.31071570.26862595X-RAY DIFFRACTION100
2.8955-2.9990.27731180.2542632X-RAY DIFFRACTION100
2.999-3.1190.32111470.23662595X-RAY DIFFRACTION100
3.119-3.26090.21361430.1982625X-RAY DIFFRACTION100
3.2609-3.43270.22071360.17782614X-RAY DIFFRACTION100
3.4327-3.64770.23111590.17362611X-RAY DIFFRACTION100
3.6477-3.92910.19291470.17242591X-RAY DIFFRACTION100
3.9291-4.3240.18841380.14142628X-RAY DIFFRACTION100
4.324-4.94860.15261320.12522638X-RAY DIFFRACTION100
4.9486-6.23080.17431180.16732652X-RAY DIFFRACTION100
6.2308-39.29550.19661470.18342655X-RAY DIFFRACTION99

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