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- PDB-3cbs: CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cbs | ||||||
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Title | CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-12 7310) | ||||||
![]() | PROTEIN (CRABP-II) | ||||||
![]() | TRANSPORT PROTEIN / RETINOIC-ACID TRANSPORT | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaudhuri, B. / Kleywegt, G.J. / Bergfors, T. / Jones, T.A. | ||||||
![]() | ![]() Title: Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids. Authors: Chaudhuri, B.N. / Kleywegt, G.J. / Broutin-L'Hermite, I. / Bergfors, T. / Senn, H. / Le Motte, P. / Partouche, O. / Jones, T.A. #1: ![]() 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. #2: 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. / Jones, T.A. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Crystallization and preliminary X-ray analysis of recombinant bovine cellular retinoic acid-binding protein. Authors: Bergfors, T. / Kleywegt, G.J. / Jones, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.2 KB | Display | ![]() |
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PDB format | ![]() | 28.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 671.7 KB | Display | ![]() |
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Full document | ![]() | 673.1 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cbrC ![]() 2cbsC ![]() 1cbsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-R12 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 20% MONOMETHYL PEG 5000 0.2 M TRIS-HCL 0.2 M LICL , pH 8.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→45 Å / Num. obs: 10051 / % possible obs: 91.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 12.2 / % possible all: 93.3 |
Reflection | *PLUS Lowest resolution: 48 Å |
Reflection shell | *PLUS % possible obs: 93.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CBS Resolution: 2→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 28049066.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 24.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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