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- PDB-6jsx: Structure of a flagellin protein, HpFlaG -

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Basic information

Entry
Database: PDB / ID: 6jsx
TitleStructure of a flagellin protein, HpFlaG
ComponentsFlagellar biosynthesis protein FlaG
KeywordsBIOSYNTHETIC PROTEIN / Helicobacter pylori / flagella
Function / homologyFlaG protein / FlaG-like superfamily / FlaG protein / Flagellar biosynthesis protein FlaG
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsTsai, J.Y. / Sun, Y.J. / Hsiao, C.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan) Taiwan
CitationJournal: J Chin Chem Soc / Year: 2019
Title: Crystal structure of the flagellin protein FlaG from Helicobacter pylori.
Authors: Tsai, J.Y. / Yeh, Y.H. / Lin, L.D. / Sun, Y.J. / Hsiao, C.D.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _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 biosynthesis protein FlaG
B: Flagellar biosynthesis protein FlaG


Theoretical massNumber of molelcules
Total (without water)16,8772
Polymers16,8772
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-29 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.411, 58.411, 231.921
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Flagellar biosynthesis protein FlaG / Flagellar protein FlaG


Mass: 8438.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BB430_02730, HPY1198_01455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B2DZ94
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28% (NH4)2SO4, 0.1M K/Na Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9641 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 7055 / % possible obs: 98.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 75.72 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.02 / Rrim(I) all: 0.058 / Χ2: 1.343 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.86.40.5746140.8840.2240.6190.77689.8
2.8-2.917.70.4066780.9410.1510.4340.76998.5
2.91-3.048.80.3226750.9810.1140.3420.79799.9
3.04-3.28.90.1716900.9930.060.1820.85100
3.2-3.48.90.1056920.9970.0370.1120.99100
3.4-3.668.80.0677140.9990.0240.0721.116100
3.66-4.038.90.0536960.9990.0190.0561.313100
4.03-4.618.50.0477250.9990.0170.051.86599.9
4.61-5.87.90.0487530.9990.0180.0512.533100
5.8-306.70.03281810.0120.0352.2997.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.7→29.206 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.34
RfactorNum. reflection% reflection
Rfree0.2699 700 10.01 %
Rwork0.2272 --
obs0.2317 6995 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.92 Å2 / Biso mean: 72.26 Å2 / Biso min: 40.05 Å2
Refinement stepCycle: final / Resolution: 2.7→29.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 0 41 1220
Biso mean---71.93 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081189
X-RAY DIFFRACTIONf_angle_d1.2291592
X-RAY DIFFRACTIONf_chiral_restr0.088182
X-RAY DIFFRACTIONf_plane_restr0.004207
X-RAY DIFFRACTIONf_dihedral_angle_d16.435479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6999-2.90820.33911280.29721157128594
2.9082-3.20050.36231370.262512231360100
3.2005-3.66280.31741400.206612571397100
3.6628-4.61190.22231400.195112711411100
4.6119-29.20720.25651550.23871387154299
Refinement TLS params.Method: refined / Origin x: -13.6135 Å / Origin y: -16.3829 Å / Origin z: -3.7017 Å
111213212223313233
T0.535 Å20.0763 Å20.0974 Å2-0.4725 Å20.1303 Å2--0.5461 Å2
L5.1892 °21.2629 °22.2467 °2-4.2149 °2-0.7106 °2--2.8728 °2
S-0.0861 Å °-0.1657 Å °-0.4542 Å °-0.1511 Å °0.0612 Å °-0.7963 Å °-0.2165 Å °-0.1172 Å °0.0033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA44 - 116
2X-RAY DIFFRACTION1allB44 - 116
3X-RAY DIFFRACTION1allS1 - 41

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