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- PDB-5gna: Crystal Structure of flagellin assembly related protein -

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Basic information

Entry
Database: PDB / ID: 5gna
TitleCrystal Structure of flagellin assembly related protein
Components
  • Flagellar hook-associated protein 2
  • Flagellar protein FliT
KeywordsGENE REGULATION / flagellin assembly related protein
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum organization / bacterial-type flagellum-dependent cell motility / protein folding / cell adhesion / extracellular region / identical protein binding / cytosol
Similarity search - Function
Flagellar protein flit. / Flagellar protein FliT / Flagellar protein FliT / 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 ...Flagellar protein flit. / Flagellar protein FliT / Flagellar protein FliT / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar protein FliT / Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, H.J. / Lee, H.H.
CitationJournal: To Be Published
Title: Crystal Structure of flagellin assembly related protein
Authors: Kim, H.J. / Lee, H.H.
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
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 protein FliT
B: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)18,4472
Polymers18,4472
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-29 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.446, 50.446, 184.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-537-

HOH

21B-577-

HOH

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Components

#1: Protein Flagellar protein FliT


Mass: 10942.468 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliT, STM1962 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1N2
#2: Protein Flagellar hook-associated protein 2 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 7504.315 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 401-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliD, flaV, flbC, STM1960 / Production host: Escherichia coli (E. coli) / References: UniProt: P16328
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 5% PEG 400, 10% isopropanol, 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11357 / % possible obs: 100 % / Redundancy: 27.1 % / Net I/σ(I): 87.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7M

3a7m


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.037 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22933 558 4.9 %RANDOM
Rwork0.21366 ---
obs0.21445 10724 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 0 193 1401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021220
X-RAY DIFFRACTIONr_bond_other_d0.0010.021197
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.9741645
X-RAY DIFFRACTIONr_angle_other_deg0.68932752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1625150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7152655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.874156
X-RAY DIFFRACTIONr_chiral_restr0.0440.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
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_it1.7934.935606
X-RAY DIFFRACTIONr_mcbond_other1.7924.928605
X-RAY DIFFRACTIONr_mcangle_it2.9647.375754
X-RAY DIFFRACTIONr_mcangle_other2.9637.383755
X-RAY DIFFRACTIONr_scbond_it2.3015.216614
X-RAY DIFFRACTIONr_scbond_other2.35.216614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.897.698892
X-RAY DIFFRACTIONr_long_range_B_refined7.18641.4861670
X-RAY DIFFRACTIONr_long_range_B_other6.62240.251552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 45 -
Rwork0.222 733 -
obs--99.87 %

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