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Yorodumi- PDB-2fr3: Crystal Structure of Cellular Retinoic Acid Binding Protein Type ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fr3 | ||||||
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Title | Crystal Structure of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.48 Angstroms Resolution | ||||||
Components | Cellular retinoic acid binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / CRABPII / Retinoic Acid / Retinoids / Beta Barrel / High Resolution | ||||||
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 / SYNCHROTRON / Rigid Body Refinement / Resolution: 1.48 Å | ||||||
Authors | Vaezeslami, S. / Geiger, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 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: Journal: Thesis 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fr3.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fr3.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2fr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/2fr3 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/2fr3 | HTTPS FTP |
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-Related structure data
Related structure data | 2frsC 2fs6C 2fs7C 2fru C: citing same article (ref.) |
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Similar 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) / Gene: CRABP2 / Plasmid: pET17-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-REA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 30% (w/v) PEG 4000, 0.1 M sodium citrate/citric acid pH 5.4, and 0.2 ammonium acetate (crystallization performed in dark room and under red light), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2005 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.48→39.81 Å / Num. all: 27332 / Num. obs: 26090 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.044 / Χ2: 2.781 / Net I/σ(I): 28.19 | |||||||||||||||
Reflection shell | Resolution: 1.48→1.53 Å / % possible obs: 96.4 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5.08 / Num. unique obs: 2590 / Χ2: 0.777 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Refinement / Resolution: 1.48→39.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.952 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.065 / 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: 15.735 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→39.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.515 Å / Total num. of bins used: 20
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