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- PDB-2cbr: CELLULAR RETINOIC ACID BINDING PROTEIN I IN COMPLEX WITH A RETINO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cbr | ||||||
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Title | CELLULAR RETINOIC ACID BINDING PROTEIN I IN COMPLEX WITH A RETINOBENZOIC ACID (AM80) | ||||||
![]() | PROTEIN (CRABP-I) | ||||||
![]() | TRANSPORT PROTEIN / RETINOIC-ACID TRANSPORT | ||||||
Function / homology | ![]() RA biosynthesis pathway / retinoic acid catabolic process / retinal binding / retinoic acid binding / retinol binding / protein-containing complex / identical protein binding / cytoplasm 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 | ![]() | 39.5 KB | Display | ![]() |
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PDB format | ![]() | 27 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cbsC ![]() 3cbsC ![]() 1cbrS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: generate Matrix: (0.231781, -0.961217, 0.149465), Vector: |
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Components
#1: Protein | Mass: 15480.392 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: MUS MUSCULUS (IDENTICAL WITH BOVINE PROTEIN) RECOMBINANT GENE Gene: MOUSE / Plasmid: PT7-1-3 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-A80 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | pH: 8 Details: IN 30% PEG4000, 0.2M LI2SO4 AND 0.1 M TRIS-HCL, PH 8.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging dropDetails: drop contained equal volume of protein and reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 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: 2.8→38.3 Å / Num. obs: 10128 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.2 / % possible all: 95.7 |
Reflection | *PLUS Lowest resolution: 38 Å |
Reflection shell | *PLUS % possible obs: 95.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CBR Resolution: 2.8→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1543984.01 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED THE STRUCTURE WAS REFINED WITH NCS CONSTRAINTS IN CNS (I.E., THE TWO MOLECULES ARE IDENTICAL).
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Displacement parameters | Biso mean: 37.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032 / 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 Num. reflection obs: 9305 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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