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- PDB-6iwy: Crystal structure of the flagellar cap protein FliD from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 6iwy
TitleCrystal structure of the flagellar cap protein FliD from Helicobacter pylori
ComponentsFlagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Bacterial flagellar cap protein
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif
Similarity search - Domain/homology
Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsCho, S.Y. / Song, W.S. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural analysis of the flagellar capping protein FliD from Helicobacter pylori.
Authors: Cho, S.Y. / Song, W.S. / Oh, H.B. / Kim, H.U. / Jung, H.S. / Yoon, S.I.
History
DepositionDec 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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 hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)43,8841
Polymers43,8841
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18250 Å2
2
A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)87,7682
Polymers87,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2500 Å2
ΔGint-11 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.510, 75.891, 133.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Flagellar hook-associated protein 2 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 43883.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: fliD, HP_0752 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96786
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M sodium citrate, pH 5-6
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 17286 / % possible obs: 99.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 34.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 4 / Num. unique obs: 824 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.319 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.297 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27672 865 5 %RANDOM
Rwork0.23981 ---
obs0.24175 16328 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 59.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 4 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222657
X-RAY DIFFRACTIONr_bond_other_d0.0060.021671
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9653594
X-RAY DIFFRACTIONr_angle_other_deg0.88834153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58227.358106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.759155
X-RAY DIFFRACTIONr_chiral_restr0.0880.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
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_it0.5211.51799
X-RAY DIFFRACTIONr_mcbond_other0.11.5757
X-RAY DIFFRACTIONr_mcangle_it0.99622847
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9463858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3274.5747
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.493 56 -
Rwork0.387 1078 -
obs--91.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7862-2.80043.41526.4951-5.169327.2303-0.23260.80670.5242-0.368-0.38250.0516-0.6368-0.08770.61510.1748-0.01120.03090.7419-0.27240.924910.37765.43517.069
22.8440.1625-0.35931.8136-0.68885.1039-0.39270.0298-0.38040.0135-0.37660.11790.7451-0.12210.76930.2842-0.07330.37740.1794-0.08280.721522.85554.93344.331
34.3739-0.9701-1.00685.41291.46233.3968-0.18130.33120.011-0.3222-0.09130.1816-0.1912-0.24680.27260.1456-0.0396-0.01180.2048-0.08090.458513.28878.60950.437
44.9775-3.4428-1.566417.85062.52045.9871-0.0585-0.2519-0.230.70620.21780.00050.12830.129-0.15930.22490.0575-0.02230.1149-0.00840.337916.71648.09171.833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 106
2X-RAY DIFFRACTION1A435 - 476
3X-RAY DIFFRACTION2A107 - 196
4X-RAY DIFFRACTION2A417 - 434
5X-RAY DIFFRACTION3A197 - 317
6X-RAY DIFFRACTION4A318 - 416

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