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- PDB-2d4y: Crystal structure of a 49K fragment of HAP1 (FlgK) -

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Basic information

Entry
Database: PDB / ID: 2d4y
TitleCrystal structure of a 49K fragment of HAP1 (FlgK)
ComponentsFlagellar hook-associated protein 1
KeywordsSTRUCTURAL PROTEIN / Multi-domain protein / alpha-helical bundle / complex all-beta folds
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 1 / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook-associated protein 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsImada, K. / Matsunami, H. / Samatey, A.F. / Nagashima, S. / Namba, K.
CitationJournal: To be Published
Title: Structure of the bacterial flagellar hook-filament junction
Authors: Imada, K. / Matsunami, H. / Yamane, M. / Samatey, A.F. / Nagashima, S. / Namba, K.
History
DepositionOct 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Flagellar hook-associated protein 1
B: Flagellar hook-associated protein 1


Theoretical massNumber of molelcules
Total (without water)99,2092
Polymers99,2092
Non-polymers00
Water13,962775
1
A: Flagellar hook-associated protein 1


Theoretical massNumber of molelcules
Total (without water)49,6041
Polymers49,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar hook-associated protein 1


Theoretical massNumber of molelcules
Total (without water)49,6041
Polymers49,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.928, 99.697, 109.645
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 Flagellar hook-associated protein 1 / HAP1


Mass: 49604.293 Da / Num. of mol.: 2 / Fragment: FK49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1J5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: 14-15% PEG 8000, 20-25% isopropanol, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11.0394
SYNCHROTRONSPring-8 BL41XU20.9797, 0.9799, 0.9735, 0.9843
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 6, 2003
MARRESEARCH2CCDFeb 6, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double-crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03941
20.97971
30.97991
40.97351
50.98431
ReflectionResolution: 2.1→75 Å / Num. all: 56302 / Num. obs: 56302 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.6 / Num. unique all: 9113 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→74.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.848 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.255 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25504 2844 5.1 %RANDOM
Rwork0.21885 ---
all0.22064 56302 --
obs0.22064 56302 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.79 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6441 0 0 775 7216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9478807
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4673848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.757151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024863
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2690.33702
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.5871
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3860.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9021.54219
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68526777
X-RAY DIFFRACTIONr_scbond_it2.48232282
X-RAY DIFFRACTIONr_scangle_it4.1284.52030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 217
Rwork0.252 3888

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