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- PDB-4zzf: Crystal structure of truncated FlgD (tetragonal form) from the hu... -

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Basic information

Entry
Database: PDB / ID: 4zzf
TitleCrystal structure of truncated FlgD (tetragonal form) from the human pathogen Helicobacter pylori
ComponentsFlagellar basal body rod modification protein
KeywordsMOTOR PROTEIN / Flagellum / Hook-caping protein
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Immunoglobulin-like - #4070 / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Basal-body rod modification protein FlgD
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1673 Å
AuthorsPulic, I. / Cendron, L. / Salamina, M. / Matkovic-Calogovic, D. / Zanotti, G.
Funding support Italy, Croatia, 3items
OrganizationGrant numberCountry
European Community's Seventh Framework Program (FP7/2007-2013)283570 Italy
PRIN 2010-2011 (MIUR) Italy
Ministry of Science, Education and Sports119-1193079-1084 Croatia
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of truncated FlgD from the human pathogen Helicobacter pylori.
Authors: Pulic, I. / Cendron, L. / Salamina, M. / Polverino de Laureto, P. / Matkovic-Calogovic, D. / Zanotti, G.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar basal body rod modification protein


Theoretical massNumber of molelcules
Total (without water)16,4491
Polymers16,4491
Non-polymers00
Water1,33374
1
A: Flagellar basal body rod modification protein

A: Flagellar basal body rod modification protein

A: Flagellar basal body rod modification protein

A: Flagellar basal body rod modification protein


Theoretical massNumber of molelcules
Total (without water)65,7944
Polymers65,7944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area3900 Å2
ΔGint-20 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.418, 76.418, 145.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

21A-363-

HOH

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Components

#1: Protein Flagellar basal body rod modification protein / Hook assembly protein / flagella (FlgD)


Mass: 16448.518 Da / Num. of mol.: 1 / Fragment: UNP residues 127-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: flgD, C694_04670, HP_0907 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25565
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62 % / Description: Prism
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Sodium acetate, Bis-Tris propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.1673→43.3801 Å / Num. obs: 11714 / % possible obs: 98.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.059 / Rsym value: 0.025 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1673→2.28 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.1 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1673→43.3801 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 586 5 %
Rwork0.1966 --
obs0.1984 11712 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1673→43.3801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 74 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081177
X-RAY DIFFRACTIONf_angle_d1.1081581
X-RAY DIFFRACTIONf_dihedral_angle_d14.173452
X-RAY DIFFRACTIONf_chiral_restr0.044166
X-RAY DIFFRACTIONf_plane_restr0.004209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1673-2.38540.32411380.26142621X-RAY DIFFRACTION95
2.3854-2.73050.28691450.24862760X-RAY DIFFRACTION100
2.7305-3.43990.28221470.22242798X-RAY DIFFRACTION100
3.4399-43.38010.19071560.16592947X-RAY DIFFRACTION100

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