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Yorodumi- PDB-2g78: Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g78 | ||||||
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Title | Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.70 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: 1.7 Å | ||||||
Authors | Vaezeslami, S. / Geiger, J.H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Protein design: reengineering cellular retinoic acid binding protein II into a rhodopsin protein mimic. Authors: Vasileiou, C. / Vaezeslami, S. / Crist, R.M. / Rabago-Smith, M. / Geiger, J.H. / Borhan, B. #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 | 2g78.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g78.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 2g78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g78 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g78 | HTTPS FTP |
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-Related structure data
Related structure data | 2g79C 2g7bC 2g7a 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: 15537.788 Da / Num. of mol.: 1 / Mutation: R132K, Y134F 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-NA / |
#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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1 M sodium citrate pH 4.8, 20% PEG 5000 and 10% DMSO, 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: Jan 12, 2003 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 1.7→40 Å / Num. all: 18359 / Num. obs: 17545 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.046 / Χ2: 0.66 / Net I/σ(I): 17.66 | |||||||||
Reflection shell | Resolution: 1.7→1.76 Å / % possible obs: 60.5 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 1085 / Χ2: 0.674 / % possible all: 60.5 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Refinement / Resolution: 1.7→39.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.17 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.107 / 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: 21.266 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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