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Yorodumi- PDB-1j7x: CRYSTAL STRUCTURE OF A FUNCTIONAL UNIT OF INTERPHOTORECEPTOR RETI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j7x | ||||||
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Title | CRYSTAL STRUCTURE OF A FUNCTIONAL UNIT OF INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN (IRBP) | ||||||
Components | INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / beta beta alpha spiral | ||||||
Function / homology | Function and homology information interphotoreceptor matrix / retinoid binding / visual perception / serine-type peptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Loew, A. / Gonzalez-Fernandez, F. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structure of the functional unit of interphotoreceptor retinoid binding protein. Authors: Loew, A. / Gonzalez-Fernandez, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j7x.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7x.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 1j7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j7x_validation.pdf.gz | 366.9 KB | Display | wwPDB validaton report |
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Full document | 1j7x_full_validation.pdf.gz | 373.2 KB | Display | |
Data in XML | 1j7x_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1j7x_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7x ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7x | 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: 33510.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pThioHis / Production host: Escherichia coli (E. coli) / Strain (production host): TOP 10 / References: UniProt: Q7SZI7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.72 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, TRIS, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→19.25 Å / Num. all: 26579 / Num. obs: 26579 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 34.56 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.846 Å / Redundancy: 2 % / Rmerge(I) obs: 0.495 / % possible all: 99.8 | ||||||||||||||||||
Reflection | *PLUS | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 99.8 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→19.25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.3 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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