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Yorodumi- PDB-3nft: Near-atomic resolution analysis of BipD- A component of the type-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nft | ||||||
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Title | Near-atomic resolution analysis of BipD- A component of the type-III secretion system of Burkholderia pseudomallei | ||||||
Components | Translocator protein bipD | ||||||
Keywords | TRANSPORT PROTEIN / Virulence / translocation | ||||||
Function / homology | IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / extracellular region / Mainly Alpha / Translocator protein BipD Function and homology information | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Pal, M. / Erskine, P.T. / Gill, R.S. / Wood, S.P. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Near-atomic resolution analysis of BipD, a component of the type III secretion system of Burkholderia pseudomallei. Authors: Pal, M. / Erskine, P.T. / Gill, R.S. / Wood, S.P. / Cooper, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nft.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nft.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nft ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nft | HTTPS FTP |
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-Related structure data
Related structure data | 2izpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33087.219 Da / Num. of mol.: 1 / Fragment: UNP Residues 8-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: bipD, BPSS1529 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63K37 |
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#2: 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: 2.1 Å3/Da / Density % sol: 41.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35% PEG 4000, 0.1M glycine, 0.02M EDTA, 0.06M cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→34.71 Å / Num. obs: 42898 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Num. unique all: 6210 / Rsym value: 0.556 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IZP Resolution: 1.51→34.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.766 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.073 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.044 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→34.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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