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Yorodumi- PDB-1cbs: CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cbs | ||||||
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Title | CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID | ||||||
Components | CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II | ||||||
Keywords | RETINOIC-ACID TRANSPORT | ||||||
Function / homology | Function and homology information positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Kleywegt, G.J. / Bergfors, T. / Jones, T.A. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. Authors: Kleywegt, G.J. / Bergfors, T. / Senn, H. / Le Motte, P. / Gsell, B. / Shudo, K. / Jones, T.A. #1: Journal: Adv.Protein Chem. / Year: 1994 Title: Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins Authors: Banaszak, L. / Winter, N. / Xu, Z. / Bernlohr, D.A. / Cowan, S.W. / Jones, T.A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Crystallisation and Preliminary X-Ray Analysis of Recombinant Bovine Cellular Retinoic Acid-Binding Protein Authors: Bergfors, T. / Kleywegt, G.J. / Jones, T.A. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallographic Studies on a Family of Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-Binding Protein in ...Title: Crystallographic Studies on a Family of Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-Binding Protein in Complex with All-Trans-Retinol Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A. #4: Journal: Embo J. / Year: 1988 Title: The Three-Dimensional Structure of P2 Myelin Protein Authors: Jones, T.A. / Bergfors, T. / Sedzik, J. / Unge, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cbs.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cbs.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cbs ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cbs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15581.802 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN CRABP-II / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P29373 |
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#2: Chemical | ChemComp-REA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 14678 / % possible obs: 90.3 % / Observed criterion σ(I): 3 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Num. measured all: 83399 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.83 Å |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 16.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.51 |