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- PDB-3k8v: Crysatl structure of a bacterial cell-surface flagellin N20C20 -

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Basic information

Entry
Database: PDB / ID: 3k8v
TitleCrysatl structure of a bacterial cell-surface flagellin N20C20
ComponentsFlagellin homolog
KeywordsSTRUCTURAL PROTEIN / FLAGELLIN / FLAGELLUM / Bacterial 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaruyama, Y. / Momma, M. / Hashimoto, W. / Murata, K.
CitationJournal: To be Published
Title: Crystal structure of N- and C-terminal regions of flagellin
Authors: Maruyama, Y. / Momma, M. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)73,2182
Polymers73,2182
Non-polymers00
Water5,386299
1
A: Flagellin homolog


Theoretical massNumber of molelcules
Total (without water)36,6091
Polymers36,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellin homolog


Theoretical massNumber of molelcules
Total (without water)36,6091
Polymers36,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Flagellin homolog

B: Flagellin homolog


Theoretical massNumber of molelcules
Total (without water)73,2182
Polymers73,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_746x+2,y-1,z+11
Buried area2400 Å2
ΔGint-20 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.676, 52.619, 64.834
Angle α, β, γ (deg.)100.32, 109.54, 111.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Flagellin homolog


Mass: 36608.805 Da / Num. of mol.: 2 / Fragment: UNP residues 21-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2PHB2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 31986 / Num. obs: 31986 / % possible obs: 96.4 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.163 / Num. unique all: 3155 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZBI

2zbi


Resolution: 2.1→29.58 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.261 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26828 1614 5 %RANDOM
Rwork0.21229 ---
obs0.2151 30366 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å21.59 Å2-0.22 Å2
2--0.67 Å20.08 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 0 299 4960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9296383
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8635645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.726.435216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73915775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0661529
X-RAY DIFFRACTIONr_chiral_restr0.0720.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023531
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4121.53169
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81625053
X-RAY DIFFRACTIONr_scbond_it1.4531527
X-RAY DIFFRACTIONr_scangle_it2.5654.51328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 111 -
Rwork0.239 2098 -
obs--90.53 %

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