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Yorodumi- PDB-1ory: FLAGELLAR EXPORT CHAPERONE IN COMPLEX WITH ITS COGNATE BINDING PARTNER -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ory | ||||||
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Title | FLAGELLAR EXPORT CHAPERONE IN COMPLEX WITH ITS COGNATE BINDING PARTNER | ||||||
Components |
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Keywords | CHAPERONE / flagellar chaperone / cytosolic export chaperone / flagellin / FliS / FliC | ||||||
Function / homology | Function and homology information bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Evdokimov, A.G. / Phan, J. / Tropea, J.E. / Routzahn, K.M. / Peters III, H.K. / Pokross, M. / Waugh, D.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type III secretion Authors: Evdokimov, A.G. / Phan, J. / Tropea, J.E. / Routzahn, K.M. / Peters III, H.K. / Pokross, M. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ory.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ory.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ory.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1ory ftp://data.pdbj.org/pub/pdb/validation_reports/or/1ory | HTTPS FTP |
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-Related structure data
Related structure data | 1orjC 1oqpS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a heterodimer |
-Components
#1: Protein | Mass: 15534.850 Da / Num. of mol.: 1 / Mutation: M12Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: FliS / Plasmid: pKM1384 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), pRIL / References: UniProt: O67806 | ||
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#2: Protein | Mass: 6173.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: FLAA OR FLIC OR AQ_1998 / Plasmid: pKM1384 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), pRIL / References: UniProt: O67803 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.81 Å3/Da / Density % sol: 74.22 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10% isopropanol, 200mM Lithium sulfate, citrate-phosphate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002 / Details: mirrors |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.45→27.7 Å / Num. all: 14386 / Num. obs: 14386 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.046 / Net I/σ(I): 15.66 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.99 / Num. unique all: 1610 / Rsym value: 0.45 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Num. obs: 13539 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.0445 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / % possible obs: 99.9 % / Redundancy: 4.8 % / Num. unique obs: 1492 / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OQP Resolution: 2.45→27.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.295 / SU ML: 0.144 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.229 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.773 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→27.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.54 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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