+Open data
-Basic information
Entry | Database: PDB / ID: 1yab | ||||||
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Title | Structure of T. maritima FliN flagellar rotor protein | ||||||
Components | chemotaxis proteinChemotaxis | ||||||
Keywords | STRUCTURAL 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 / plasma membrane Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Hill, C.P. / Blair, D.F. / Brown, P.N. / Mathews, M.A.A. / Joss, L.A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yab.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yab.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1yab ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1yab | HTTPS FTP |
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-Related structure data
Related structure data | 1o6aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
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Details | Two 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. |
-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979277 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979277 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O6A.pdb 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.247 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→19.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 668 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.397→3.581 Å / Total num. of bins used: 10
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