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- PDB-5b3d: Structure of a flagellar type III secretion chaperone, FlgN -

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Basic information

Entry
Database: PDB / ID: 5b3d
TitleStructure of a flagellar type III secretion chaperone, FlgN
ComponentsFlagella synthesis protein FlgN
KeywordsPROTEIN TRANSPORT / flagellar type III secretion / export chaperone / four-stranded coiled coil
Function / homologyFlgN-like protein / FlgN-like superfamily / FlgN protein / bacterial-type flagellum assembly / cytoplasm / Flagella synthesis protein FlgN
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsNakanishi, Y. / Kinoshita, M. / Namba, K. / Minamino, T. / Imada, K.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15H02386 Japan
Japan Society for the Promotion of Science26293097 Japan
Japan Society for the Promotion of Science25000013 Japan
MEXT23115008 Japan
MEXT24117004 Japan
MEXT25121718 Japan
MEXT15H01640 Japan
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Rearrangements of alpha-helical structures of FlgN chaperone control the binding affinity for its cognate substrates during flagellar type III export
Authors: Kinoshita, M. / Nakanishi, Y. / Furukawa, Y. / Namba, K. / Imada, K. / Minamino, T.
History
DepositionFeb 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagella synthesis protein FlgN
B: Flagella synthesis protein FlgN
C: Flagella synthesis protein FlgN
D: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)64,5944
Polymers64,5944
Non-polymers00
Water6,269348
1
A: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Flagella synthesis protein FlgN
B: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)32,2972
Polymers32,2972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-68 kcal/mol
Surface area13610 Å2
MethodPISA
6
C: Flagella synthesis protein FlgN
D: Flagella synthesis protein FlgN


Theoretical massNumber of molelcules
Total (without water)32,2972
Polymers32,2972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-68 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)83.551, 91.608, 94.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDepositors state that FlgN is in an equilibrium between monomer and dimer in solution and the equilibrium is confirmed by sedimentation equilibrium method.

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Components

#1: Protein
Flagella synthesis protein FlgN


Mass: 16148.458 Da / Num. of mol.: 4 / Fragment: UNP residues 2-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: flgN, STM1171 / Plasmid: pET3c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A1J7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3-14% (w/v) Glycerol, 0.1 M Tris-HCl pH8.5 and 1.25-1.4M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.1 Å / Num. obs: 32802 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.9 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→38.231 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.99
RfactorNum. reflection% reflection
Rfree0.2402 1640 5.01 %
Rwork0.2074 --
obs0.209 32734 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 0 348 4047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033772
X-RAY DIFFRACTIONf_angle_d0.5295095
X-RAY DIFFRACTIONf_dihedral_angle_d16.0461463
X-RAY DIFFRACTIONf_chiral_restr0.02580
X-RAY DIFFRACTIONf_plane_restr0.002677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.29651280.23812341X-RAY DIFFRACTION91
2.3677-2.44410.29351320.23212572X-RAY DIFFRACTION100
2.4441-2.53140.2571360.22052590X-RAY DIFFRACTION100
2.5314-2.63280.23631360.21592573X-RAY DIFFRACTION100
2.6328-2.75260.29791310.23072573X-RAY DIFFRACTION100
2.7526-2.89760.24661400.22142564X-RAY DIFFRACTION100
2.8976-3.07910.26071420.20512595X-RAY DIFFRACTION100
3.0791-3.31670.23251340.20722613X-RAY DIFFRACTION100
3.3167-3.65030.20411330.1872629X-RAY DIFFRACTION100
3.6503-4.17790.23521360.18462623X-RAY DIFFRACTION100
4.1779-5.26150.21291410.19642654X-RAY DIFFRACTION100
5.2615-38.23630.23051510.21712767X-RAY DIFFRACTION100

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