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- PDB-3c12: Crystal Structure of FlgD from Xanthomonas campestris: Insights i... -

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Basic information

Entry
Database: PDB / ID: 3c12
TitleCrystal Structure of FlgD from Xanthomonas campestris: Insights into the Hook Capping Essential for Flagellar Assembly
ComponentsFlagellar protein
KeywordsBIOSYNTHETIC PROTEIN / FlgD / hook capping / Xanthomonas campestris / Ig-like domain / Fn-III domain / tudor-like domain / flagellar biogenesis / Flagellum
Function / homology
Function and homology information


bacterial-type flagellum organization
Similarity search - Function
SH3 type barrels. - #910 / Immunoglobulin-like - #4070 / FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / SH3 type barrels. / Roll ...SH3 type barrels. - #910 / Immunoglobulin-like - #4070 / FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / SH3 type barrels. / Roll / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Basal-body rod modification protein FlgD
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsKuo, W.-T. / Chin, K.-H. / Lo, W.-T. / Chou, S.-H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the C-terminal domain of a flagellar hook-capping protein from Xanthomonas campestris
Authors: Kuo, W.-T. / Chin, K.-H. / Lo, W.-T. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 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 protein


Theoretical massNumber of molelcules
Total (without water)13,7381
Polymers13,7381
Non-polymers00
Water55831
1
A: Flagellar protein

A: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)27,4762
Polymers27,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+3/21
Unit cell
Length a, b, c (Å)116.710, 116.710, 71.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Flagellar protein / FlgD


Mass: 13738.245 Da / Num. of mol.: 1 / Fragment: UNP Residues 84-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8P9B5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3

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Sample preparation

CrystalDensity Matthews: 5.138965 Å3/Da / Density % sol: 76.065216 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 11527 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 11 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / Num. unique all: 11527 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.51→29.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 394950.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1846 9.3 %RANDOM
Rwork0.257 ---
obs0.257 11527 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.627 Å2 / ksol: 0.376483 e/Å3
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å26.47 Å20 Å2
2---1.91 Å20 Å2
3---3.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.51→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 0 31 998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.51→2.61 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.272 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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