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- PDB-6rgv: Truncated FljB phase 2 flagellin -

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Basic information

Entry
Database: PDB / ID: 6rgv
TitleTruncated FljB phase 2 flagellin
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / Flagellum / Methylation / Bacterial motility / Cell adhesion
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / bacterial-type flagellum filament / The IPAF inflammasome / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
: / Flagellin, barrel domain / Flagellin D3 / Flagellin D3 domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellin / Phase 2 flagellin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLunelli, M. / Lokareddy, R.K. / Kolbe, M.
Citation
Journal: Nat Commun / Year: 2020
Title: Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion.
Authors: Horstmann, J.A. / Lunelli, M. / Cazzola, H. / Heidemann, J. / Kuhne, C. / Steffen, P. / Szefs, S. / Rossi, C. / Lokareddy, R.K. / Wang, C. / Lemaire, L. / Hughes, K.T. / Uetrecht, C. / ...Authors: Horstmann, J.A. / Lunelli, M. / Cazzola, H. / Heidemann, J. / Kuhne, C. / Steffen, P. / Szefs, S. / Rossi, C. / Lokareddy, R.K. / Wang, C. / Lemaire, L. / Hughes, K.T. / Uetrecht, C. / Schluter, H. / Grassl, G.A. / Stradal, T.E.B. / Rossez, Y. / Kolbe, M. / Erhardt, M.
#1: Journal: Mol.Microbiol. / Year: 2019
Title: Role of flagellar hydrogen bonding in Salmonella motility and flagellar polymorphic transition.
Authors: Wang, C. / Lunelli, M. / Zschieschang, E. / Bosse, J.B. / Thuenauer, R. / Kolbe, M.
History
DepositionApr 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: 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: Flagellin


Theoretical massNumber of molelcules
Total (without water)44,6061
Polymers44,6061
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.468, 38.280, 124.690
Angle α, β, γ (deg.)90.000, 103.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Flagellin


Mass: 44605.570 Da / Num. of mol.: 1 / Mutation: A190V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: fljB, SL1344_2756 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3NEZ8, UniProt: P52616*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris (pH 8.5), 20% (w/v) PEG4000, 24% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30567 / % possible obs: 98.7 % / Redundancy: 5.561 % / Biso Wilson estimate: 33.338 Å2 / Rmerge F obs: 0.118 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.106 / Χ2: 1.058 / Net I/σ(I): 11.25 / Num. measured all: 169968 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2-2.054.6510.6732.2619270.75286
2.05-2.14.9670.5073.1122030.56598.8
2.1-2.175.1280.4143.8821280.46199.3
2.17-2.235.3090.3544.4520790.39399.9
2.23-2.35.4490.2726.2120140.30299.7
2.3-2.395.5570.2845.9119990.31499.9
2.39-2.485.7410.2227.3618460.245100
2.48-2.585.8120.1978.2518430.21799.9
2.58-2.695.9550.15810.3217630.17499.9
2.69-2.825.9650.13212.2716450.14599.8
2.82-2.985.9350.11414.2816120.12699.9
2.98-3.165.9090.09816.0715230.10899.9
3.16-3.375.8290.08418.2814090.093100
3.37-3.645.7140.07620.4713180.08399.8
3.64-3.995.7050.06622.0712540.07399.9
3.99-4.465.6920.06323.1311120.06999.6
4.46-5.155.7920.05724.159870.063100
5.15-6.315.8480.05623.58530.06199.8
6.31-8.935.7330.04524.556640.04999.8
8.93-505.4180.03625.663880.0499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSDecember 6, 2010data reduction
XSCALEDecember 6, 2010data scaling
PHASER2.5.2phasing
CNS1.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IO1

1io1


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2585 1529 5 %
Rwork0.2127 --
obs-30567 98.8 %
Solvent computationBsol: 36.0107 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 102.03 Å2 / Biso mean: 34.7588 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1--6.642 Å20 Å2-7.643 Å2
2--0.303 Å20 Å2
3---6.339 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.21 Å
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 0 299 3237
Biso mean---35.98 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.325
X-RAY DIFFRACTIONc_mcbond_it3.2582
X-RAY DIFFRACTIONc_scbond_it6.734.5
X-RAY DIFFRACTIONc_mcangle_it4.153
X-RAY DIFFRACTIONc_scangle_it7.976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.070.32721360.28412589272589.5
2.07-2.150.29491530.24122894304799
2.15-2.250.25831530.2232902305599.8
2.25-2.370.30961530.25562906305999.9
2.37-2.510.31811530.2472912306599.8
2.51-2.710.3121540.25212927308199.9
2.71-2.980.29941540.23432930308499.9
2.98-3.410.26891540.224429333087100
3.41-4.30.22761580.18142990314899.9
4.3-500.19751610.16883055321699.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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