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Yorodumi- PDB-1eq6: 1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE SACCHAROMYCES CE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eq6 | ||||||
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Title | 1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE RAN-BINDING PROTEIN MOG1P | ||||||
Components | MOG1P | ||||||
Keywords | PROTEIN TRANSPORT / alpha-beta | ||||||
Function / homology | Function and homology information regulation of membrane depolarization / sodium channel regulator activity / mRNA transport / guanyl-nucleotide exchange factor activity / small GTPase binding / protein import into nucleus / transmembrane transporter binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD PLUS SIR / Resolution: 1.9 Å | ||||||
Authors | Stewart, M. / Baker, R.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: 1.9 A resolution crystal structure of the Saccharomyces cerevisiae Ran-binding protein Mog1p. Authors: Stewart, M. / Baker, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eq6.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eq6.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1eq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eq6_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 1eq6_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 1eq6_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1eq6_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eq6 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eq6 | 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: 21160.680 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PMW172 / Production host: Escherichia coli (E. coli) / References: UniProt: P47123 |
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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: 2.73 Å3/Da / Density % sol: 48.5 % / Description: 3A PHASES OBTAINED FROM SE-MET MAD PLUS Hg SIR | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG4000, glycerol, sodium acetate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 49.5 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 5.6 / Method: vapor diffusionDetails: Baker, R.P.,(2000) Acta Crystallog. Sect., D56, 229. | |||||||||||||||||||||||||
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: ESRF / Beamline: ID2 / Wavelength: 0.9887 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9887 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 18951 / Num. obs: 18625 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2679 / Rsym value: 0.146 / % possible all: 98.5 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.146 |
-Processing
Software |
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Refinement | Method to determine structure: MAD PLUS SIR / Resolution: 1.9→20 Å / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: used maximum likelihood target "mlf"
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Displacement parameters | Biso mean: 33.32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.268 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.227 / Rfactor obs: 0.227 |