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Yorodumi- PDB-1aua: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P FROM SACCHAROMYCES C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aua | ||||||
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Title | PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P FROM SACCHAROMYCES CEREVISIAE | ||||||
Components | PHOSPHATIDYLINOSITOL TRANSFER PROTEIN SEC14P | ||||||
Keywords | PHOSPHOLIPID-BINDING PROTEIN / PERIPHERAL GOLGI MEMBRANE PROTEIN / PHOSPHOLIPID EXCHANGE / GOLGI-DERIVED SECRETORY VESICLE BIOGENESIS | ||||||
Function / homology | Function and homology information negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport ...negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport / Golgi membrane / Golgi apparatus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Sha, B. / Phillips, S.E. / Bankaitis, V.A. / Luo, M. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Crystal structure of the Saccharomyces cerevisiae phosphatidylinositol-transfer protein. Authors: Sha, B. / Phillips, S.E. / Bankaitis, V.A. / Luo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aua.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aua.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 1aua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aua_validation.pdf.gz | 818.5 KB | Display | wwPDB validaton report |
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Full document | 1aua_full_validation.pdf.gz | 826 KB | Display | |
Data in XML | 1aua_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 1aua_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/1aua ftp://data.pdbj.org/pub/pdb/validation_reports/au/1aua | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34045.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC14 / Plasmid: PQE-31 / Gene (production host): SEC14 / Production host: Escherichia coli (E. coli) / Strain (production host): KK2186 / References: UniProt: P24280 | ||
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#2: Sugar | #3: 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: 3.6 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: 3% PEG 3350, 1% N-OCTYL B-D-GLUCOPYRANOSIDE, 10 MM HEPES, 150MM KCL, PH 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 16736 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.051 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.5→2.67 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 8 / Rsym value: 0.265 / % possible all: 80 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 80 % / Rmerge(I) obs: 0.265 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE PARAMETER AND TOPOLOGY FILES ARE AVAILABLE FROM DR. B.SHA.
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Displacement parameters | Biso mean: 47.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.354 |