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- PDB-2zbi: Crystal structure of a bacterial cell-surface flagellin -

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Basic information

Entry
Database: PDB / ID: 2zbi
TitleCrystal structure of a bacterial cell-surface flagellin
ComponentsFlagellin homolog
KeywordsSTRUCTURAL PROTEIN / flagellin / Flagellum
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Alpha-Beta Plaits - #2120 / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain ...Alpha-Beta Plaits - #2120 / f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / Flagellin hook, IN motif / Flagellin hook IN motif / 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 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMaruyama, Y.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure of a novel bacterial cell-surface flagellin binding to a polysaccharide
Authors: Maruyama, Y. / Momma, M. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionOct 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin homolog
B: Flagellin homolog


Theoretical massNumber of molelcules
Total (without water)60,9632
Polymers60,9632
Non-polymers00
Water6,197344
1
A: Flagellin homolog


Theoretical massNumber of molelcules
Total (without water)30,4821
Polymers30,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellin homolog


Theoretical massNumber of molelcules
Total (without water)30,4821
Polymers30,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.486, 52.166, 76.198
Angle α, β, γ (deg.)99.11, 93.90, 107.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Flagellin homolog / flagellin homologue p5


Mass: 30481.611 Da / Num. of mol.: 2 / Fragment: Residues UNP 55-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Gene: FliC / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3) / References: UniProt: Q2PHB2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 5000 MME, 0.2M Ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97906 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 61347 / % possible obs: 97.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 17.127 Å2 / Rsym value: 0.051 / Net I/σ(I): 23.93
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 6.74 / Rsym value: 0.19

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.68 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.853 / SU B: 6.2 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 1547 5 %RANDOM
Rwork0.19648 ---
obs0.2008 29294 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.256 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.05 Å2-0.04 Å2
2---0.1 Å2-0.05 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 0 344 4198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223874
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9245279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2785536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74326.854178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16515623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg191520
X-RAY DIFFRACTIONr_chiral_restr0.1440.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022926
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.22098
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22749
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0331.52697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59924194
X-RAY DIFFRACTIONr_scbond_it3.0431289
X-RAY DIFFRACTIONr_scangle_it4.6984.51082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 117 -
Rwork0.25 1964 -
obs--89.97 %

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