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Yorodumi- PDB-3loi: Crystal structures of Cupin superfamily BbDUF985 from Branchiosto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3loi | ||||||
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Title | Crystal structures of Cupin superfamily BbDUF985 from Branchiostoma belcheri tsingtauense in the apo and GDP-bound forms | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Beta barrel | ||||||
Function / homology | Function and homology information Cupin domain of unknown function DUF985 / Uncharacterized protein YML079W-like / Cupin superfamily (DUF985) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Branchiostoma belcheri tsingtauense (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zou, C.Z. / Du, Y. / He, Y.-X. / Saren, G. / Zhang, X. / Chen, Y. / Zhang, S.-C. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Crystal structures of the apo and GDP-bound forms of a cupin-like protein BbDUF985 from Branchiostoma belcheri tsingtauense Authors: Zou, C.Z. / Du, Y. / He, Y.-X. / Saren, G. / Zhang, X. / Chen, Y. / Zhang, S.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3loi.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3loi.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 3loi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3loi_validation.pdf.gz | 423.9 KB | Display | wwPDB validaton report |
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Full document | 3loi_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 3loi_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 3loi_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/3loi ftp://data.pdbj.org/pub/pdb/validation_reports/lo/3loi | HTTPS FTP |
-Related structure data
Related structure data | 3lzzC 1yudS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19558.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Branchiostoma belcheri tsingtauense (invertebrata) Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WRH7 |
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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: 4.64 Å3/Da / Density % sol: 73.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2.0M ammonium sulfate, 0.1M sodium acetate trihydate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 21913 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1071 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YUD Resolution: 2.1→33.396 Å / SU ML: 0.32 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.435 Å2 / ksol: 0.333 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→33.396 Å
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Refine LS restraints |
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LS refinement shell |
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