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- PDB-5npy: Crystal structure of Helicobacter pylori flagellar hook protein FlgE2 -

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Basic information

Entry
Database: PDB / ID: 5npy
TitleCrystal structure of Helicobacter pylori flagellar hook protein FlgE2
ComponentsFlagellar basal body protein
KeywordsMOTOR PROTEIN / Helicobactyer pylori / flagellum / hook
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Flagellar hook protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.292 Å
AuthorsLoconte, V. / Zanotti, G. / Kekez, I. / Matkovic-Calogovic, D.
CitationJournal: FEBS J. / Year: 2017
Title: Structural characterization of FlgE2 protein from Helicobacter pylori hook.
Authors: Loconte, V. / Kekez, I. / Matkovic-Calogovic, D. / Zanotti, G.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 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 basal body protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0272
Polymers68,9051
Non-polymers1221
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint3 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.209, 49.592, 238.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flagellar basal body protein


Mass: 68904.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: flgE-2, HPG27_859 / Plasmid: pETit-hp0908 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z7R4
#2: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Potassium Thiocyanate, 0.1 M Bis-Tris Propane pH 8.5, 20% w/v PEG3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.8729
SYNCHROTRONESRF ID23-120.98127
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELMay 12, 2016
DECTRIS PILATUS3 S 6M2PIXELMar 21, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.87291
20.981271
ReflectionResolution: 2.29→48.551 Å / Num. obs: 23979 / % possible obs: 98.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.076 / Net I/σ(I): 9.7
Reflection shellResolution: 2.29→2.4 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3106 / Rpim(I) all: 0.362 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.292→48.551 Å / SU ML: 0.35 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 28.21
RfactorNum. reflection% reflection
Rfree0.2661 2133 4.97 %
Rwork0.1881 --
obs0.192 23686 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.292→48.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 8 308 4031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083792
X-RAY DIFFRACTIONf_angle_d0.9955112
X-RAY DIFFRACTIONf_dihedral_angle_d15.2792311
X-RAY DIFFRACTIONf_chiral_restr0.058553
X-RAY DIFFRACTIONf_plane_restr0.007669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2922-2.34550.28871060.24042091X-RAY DIFFRACTION74
2.3455-2.40420.3331480.24072786X-RAY DIFFRACTION99
2.4042-2.46920.37551490.25862765X-RAY DIFFRACTION99
2.4692-2.54180.32851460.25152794X-RAY DIFFRACTION99
2.5418-2.62390.36731460.25562778X-RAY DIFFRACTION99
2.6239-2.71770.31681360.25182756X-RAY DIFFRACTION98
2.7177-2.82650.32821380.24742712X-RAY DIFFRACTION98
2.8265-2.95510.29991480.2342777X-RAY DIFFRACTION99
2.9551-3.11080.32081450.21072826X-RAY DIFFRACTION99
3.1108-3.30570.24131450.18622795X-RAY DIFFRACTION99
3.3057-3.56090.31211410.1792755X-RAY DIFFRACTION99
3.5609-3.91910.25041440.16932719X-RAY DIFFRACTION97
3.9191-4.48580.19881450.12982707X-RAY DIFFRACTION97
4.4858-5.65030.20541450.1322769X-RAY DIFFRACTION99
5.6503-48.56230.20881510.17132779X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 36.8348 Å / Origin y: -0.1189 Å / Origin z: 227.6481 Å
111213212223313233
T0.1647 Å20.003 Å20.022 Å2-0.1652 Å2-0.0042 Å2--0.1703 Å2
L0.1009 °2-0.0833 °20.0204 °2-0.1709 °2-0.1689 °2--0.5528 °2
S0.0461 Å °0.0088 Å °-0.0151 Å °0.0219 Å °0.0423 Å °-0.0266 Å °-0.0914 Å °-0.0125 Å °0.0122 Å °
Refinement TLS groupSelection details: all

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