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Yorodumi- PDB-1opb: THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1opb | ||||||
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Title | THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II | ||||||
Components | CELLULAR RETINOL BINDING PROTEIN II | ||||||
Keywords | RETINOL TRANSPORT | ||||||
Function / homology | Function and homology information Retinoid metabolism and transport / retinal binding / retinol metabolic process / retinol binding / fatty acid transport / fatty acid binding / lipid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Winter, N. / Banaszak, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Crystal structures of holo and apo-cellular retinol-binding protein II. Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A TEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY AN ELEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1opb.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1opb.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 1opb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1opb_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 1opb_full_validation.pdf.gz | 500.9 KB | Display | |
Data in XML | 1opb_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1opb_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1opb ftp://data.pdbj.org/pub/pdb/validation_reports/op/1opb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15606.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P06768 #2: Chemical | ChemComp-RET / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 17.5 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 23764 / % possible obs: 75 % / Num. measured all: 57160 / Rmerge(I) obs: 0.0642 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.173 / Rfactor obs: 0.173 / Highest resolution: 1.9 Å Details: DATA WAS COLLECTED TO 2.1 ANGSTROMS RESOLUTION ON SIEMENS AREA DETECTOR. THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING THE COORDINATES OF CELLULAR RETINOL BINDING PROTEIN AS A MODEL. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Rfactor obs: 0.173 / Num. reflection obs: 52976 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.336 |