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- PDB-5h72: Structure of the periplasmic domain of FliP -

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Basic information

Entry
Database: PDB / ID: 5h72
TitleStructure of the periplasmic domain of FliP
ComponentsFlagellar biosynthetic protein FliP
KeywordsBIOSYNTHETIC PROTEIN / Flagellar protein export
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Flagellar transport protein FliP / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2.
Similarity search - Domain/homology
Flagellar biosynthetic protein FliP
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsFukumura, T. / Kawaguchi, T. / Saijo-Hamano, Y. / Namba, K. / Minamino, T. / Imada, K.
Citation
Journal: PLoS Biol. / Year: 2017
Title: Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex
Authors: Fukumura, T. / Makino, F. / Dietsche, T. / Kinoshita, M. / Kato, T. / Wagner, S. / Namba, K. / Imada, K. / Minamino, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and preliminary X-ray analysis of the periplasmic domain of FliP, an integral membrane component of the bacterial flagellar type III protein-export apparatus
Authors: Fukumura, T. / Furukawa, Y. / Kawaguchi, T. / Saijo-Hamano, Y. / Namba, K. / Imada, K. / Minamino, T.
History
DepositionNov 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 20, 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 biosynthetic protein FliP
B: Flagellar biosynthetic protein FliP
C: Flagellar biosynthetic protein FliP
D: Flagellar biosynthetic protein FliP
E: Flagellar biosynthetic protein FliP
F: Flagellar biosynthetic protein FliP
G: Flagellar biosynthetic protein FliP
H: Flagellar biosynthetic protein FliP


Theoretical massNumber of molelcules
Total (without water)75,4708
Polymers75,4708
Non-polymers00
Water7,080393
1
A: Flagellar biosynthetic protein FliP
B: Flagellar biosynthetic protein FliP
C: Flagellar biosynthetic protein FliP
D: Flagellar biosynthetic protein FliP


Theoretical massNumber of molelcules
Total (without water)37,7354
Polymers37,7354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-29 kcal/mol
Surface area15190 Å2
MethodPISA
2
E: Flagellar biosynthetic protein FliP
F: Flagellar biosynthetic protein FliP
G: Flagellar biosynthetic protein FliP
H: Flagellar biosynthetic protein FliP


Theoretical massNumber of molelcules
Total (without water)37,7354
Polymers37,7354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.880, 114.880, 193.781
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

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Components

#1: Protein
Flagellar biosynthetic protein FliP


Mass: 9433.692 Da / Num. of mol.: 8 / Fragment: periplasmic fragment, UNP residues 110-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: fliP, TM_0698, Tmari_0698 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZG2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 0.1M phosphate-citrate pH 4.4, 36% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 2, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→43.6 Å / Num. obs: 30262 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→42.923 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1518 5.05 %
Rwork0.2112 --
obs0.2138 30080 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→42.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 0 393 4729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064408
X-RAY DIFFRACTIONf_angle_d0.8595928
X-RAY DIFFRACTIONf_dihedral_angle_d15.9221664
X-RAY DIFFRACTIONf_chiral_restr0.032656
X-RAY DIFFRACTIONf_plane_restr0.004784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.30161310.22692545X-RAY DIFFRACTION100
2.4775-2.5660.31751210.21822567X-RAY DIFFRACTION100
2.566-2.66870.2651410.20812560X-RAY DIFFRACTION100
2.6687-2.79020.26121420.19932559X-RAY DIFFRACTION100
2.7902-2.93730.24611410.20462565X-RAY DIFFRACTION100
2.9373-3.12120.23811330.20242587X-RAY DIFFRACTION100
3.1212-3.36210.26661330.20162596X-RAY DIFFRACTION100
3.3621-3.70030.23091670.1882584X-RAY DIFFRACTION100
3.7003-4.23540.23341290.19522633X-RAY DIFFRACTION100
4.2354-5.33450.2431460.19912659X-RAY DIFFRACTION100
5.3345-42.93030.34361340.28652707X-RAY DIFFRACTION95

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