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- PDB-1yab: Structure of T. maritima FliN flagellar rotor protein -

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Basic information

Entry
Database: PDB / ID: 1yab
TitleStructure of T. maritima FliN flagellar rotor protein
Componentschemotaxis protein
KeywordsSTRUCTURAL PROTEIN / Thermotoga maritima / flagellar motor / rotor / FliN / FliY
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / hydrolase activity / plasma membrane
Similarity search - Function
CheC-like protein / CheC-like family / Surface presentation of antigens (SPOA) / SpoA-like / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily ...CheC-like protein / CheC-like family / Surface presentation of antigens (SPOA) / SpoA-like / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Roll / Mainly Beta
Similarity search - Domain/homology
: / CheC, inhibitor of MCP methylation / FliN fusion protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHill, C.P. / Blair, D.F. / Brown, P.N. / Mathews, M.A.A. / Joss, L.A.
CitationJournal: J.BACTERIOL. / Year: 2005
Title: Crystal Structure of the Flagellar Rotor Protein FliN from Thermotoga maritima
Authors: Brown, P.N. / Mathews, M.A.A. / Joss, L.A. / Hill, C.P. / Blair, D.F.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 25, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chemotaxis protein
B: chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,6012
Non-polymers00
Water00
1
A: chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)9,8011
Polymers9,8011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)9,8011
Polymers9,8011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: chemotaxis protein
B: chemotaxis protein

A: chemotaxis protein
B: chemotaxis protein


Theoretical massNumber of molelcules
Total (without water)39,2024
Polymers39,2024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area13430 Å2
ΔGint-97 kcal/mol
Surface area16490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.173, 100.173, 87.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 68 - 152 / Label seq-ID: 1 - 85

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTwo molecules of FliN constructu containing residues 68 to 154 form the asymmetric unit. The two monomers interact over a large surface, with intertwined elements, each forming a saddle shape that interlocks with the other.

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Components

#1: Protein chemotaxis protein / FliN


Mass: 9800.546 Da / Num. of mol.: 2 / Fragment: residues 68-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Production host: Escherichia coli (E. coli) / References: GenBank: 15644624, UniProt: A0A0F6AJI7*PLUS

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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: 3.7 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 18% MPD, 100mM MES buffer, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979277 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979277 Å / Relative weight: 1
ReflectionResolution: 3.4→87.7 Å / Num. all: 7246 / Num. obs: 7246 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rsym value: 0.07 / Net I/σ(I): 7.3
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 996 / Rsym value: 0.289 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O6A.pdb

1o6a


Resolution: 3.4→19.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 24.248 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.738 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28624 340 4.7 %RANDOM
Rwork0.22437 ---
all0.22735 7246 --
obs0.22735 6906 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.247 Å2
Baniso -1Baniso -2Baniso -3
1-6.52 Å23.26 Å20 Å2
2--6.52 Å20 Å2
3----9.78 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 0 1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221360
X-RAY DIFFRACTIONr_angle_refined_deg1.762.0251834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7385170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.64224.5151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.9715289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9031512
X-RAY DIFFRACTIONr_chiral_restr0.1190.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02934
X-RAY DIFFRACTIONr_nbd_refined0.2640.2637
X-RAY DIFFRACTIONr_nbtor_refined0.3260.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.222
X-RAY DIFFRACTIONr_mcbond_it0.7461.5876
X-RAY DIFFRACTIONr_mcangle_it1.39621400
X-RAY DIFFRACTIONr_scbond_it1.7083511
X-RAY DIFFRACTIONr_scangle_it3.3534.5434
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 668 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.710.5
medium thermal0.422
LS refinement shellResolution: 3.397→3.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.417 53 -
Rwork0.337 996 -
obs--99.71 %

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