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- PDB-4cfi: 3D structure of FliC from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 4cfi
Title3D structure of FliC from Burkholderia pseudomallei
ComponentsFLAGELLIN
KeywordsSTRUCTURAL PROTEIN / FLAGELLA / EPITOPE / IMMUNE RESPONSE
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, D2 domain / Flagellin, D2 domain / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal 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 ...Flagellin, D2 domain / Flagellin, D2 domain / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLassaux, P. / Peri, C. / Ferrer-Navarro, M. / Gourlay, L.J. / Conchillo-Sole, O. / Daura, X. / Colombo, G. / Bolognesi, M.
CitationJournal: Plos Negl Trop Dis / Year: 2015
Title: Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia Pseudomallei Flagellin.
Authors: Nithichanon, A. / Rinchai, D. / Gori, A. / Lassaux, P. / Peri, C. / Conchillio-Sole, O. / Ferrer-Navarro, M. / Gourlay, L.J. / Nardini, M. / Vila, J. / Daura, X. / Colombo, G. / Bolognesi, M. ...Authors: Nithichanon, A. / Rinchai, D. / Gori, A. / Lassaux, P. / Peri, C. / Conchillio-Sole, O. / Ferrer-Navarro, M. / Gourlay, L.J. / Nardini, M. / Vila, J. / Daura, X. / Colombo, G. / Bolognesi, M. / Lertmemonkolchai, G.
History
DepositionNov 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAGELLIN


Theoretical massNumber of molelcules
Total (without water)25,8991
Polymers25,8991
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.470, 72.780, 125.570
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 FLAGELLIN / FLIC


Mass: 25899.211 Da / Num. of mol.: 1 / Fragment: RESIDUES 69-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70944
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 25% PEG 6000 AND 0.1 M LITHIUM CHLORIDE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731
DetectorDate: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.3→24.26 Å / Num. obs: 51380 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3K8V, 1IO1 AND 3V47

3k8v

1io1

3v47


Resolution: 1.3→23.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.346 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16461 2753 5.1 %RANDOM
Rwork0.13633 ---
obs0.13774 54199 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 279 2092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192175
X-RAY DIFFRACTIONr_bond_other_d0.0020.022015
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9283011
X-RAY DIFFRACTIONr_angle_other_deg0.76334643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2385332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48827.79186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50415351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.324155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022828
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02509
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11.1271232
X-RAY DIFFRACTIONr_mcbond_other1.0991.1261231
X-RAY DIFFRACTIONr_mcangle_it1.5421.7031596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7321.323943
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.38634190
X-RAY DIFFRACTIONr_sphericity_free21.047557
X-RAY DIFFRACTIONr_sphericity_bonded8.02154369
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 178 -
Rwork0.16 3688 -
obs--99.08 %

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