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- PDB-2fs6: Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fs6 | ||||||
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Title | Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.35 Angstroms Resolution | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | TRANSPORT PROTEIN / CRABPII / Retinoic Acid / Retinoids / Beta Barrel / High Resolution | ||||||
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 | ![]() ![]() | ||||||
![]() | Vaezeslami, S. / Geiger, J.H. | ||||||
![]() | ![]() Title: The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation. Authors: Vaezeslami, S. / Mathes, E. / Vasileiou, C. / Borhan, B. / Geiger, J.H. #1: ![]() Title: Determining crystal structures of proteins and protein complexes by X-ray crystallography: X-ray crystallographic studies of the mutants of cellular retinoic acid binding protein type II ...Title: Determining crystal structures of proteins and protein complexes by X-ray crystallography: X-ray crystallographic studies of the mutants of cellular retinoic acid binding protein type II toward designing a mimic of rhodopsin Authors: Vaezeslami, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.3 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 446.7 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fr3C ![]() 2frsC ![]() 2fs7C ![]() 2frr ![]() 2fru ![]() 2fs0 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15581.802 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% (w/v) PEG 8000 (4000), 0.1 M TRIS-HCl pH 8.0 (8.5), and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 56961 / Num. obs: 50380 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.042 / Χ2: 0.591 / Net I/σ(I): 14.56 |
Reflection shell | Resolution: 1.35→1.4 Å / % possible obs: 56.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 3219 / Χ2: 0.517 / % possible all: 56.5 |
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Processing
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Refinement | Method to determine structure: Rigid body refinement / Resolution: 1.35→17.24 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.636 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→17.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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