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Yorodumi- PDB-3d95: Crystal Structure of the R132K:Y134F:R111L:L121E:T54V Mutant of A... -
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-Basic information
Entry | Database: PDB / ID: 3d95 | ||||||
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Title | Crystal Structure of the R132K:Y134F:R111L:L121E:T54V Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.20 Angstroms Resolution | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / CRABPII / RETINOIC ACID / RETINOIDS / BETA BARREL / HIGH RESOLUTION / MUTANT / Cytoplasm / Nucleus / Retinol-binding / Transport / Vitamin A | ||||||
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: 1.2 Å | ||||||
Authors | Vaezeslami, S. / Geiger, J.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding. Authors: Vaezeslami, S. / Jia, X. / 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 | 3d95.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d95.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 3d95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d95 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d95 | HTTPS FTP |
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-Related structure data
-Links
-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: 15507.735 Da / Num. of mol.: 2 / Mutation: R132K, Y134F, R111L, L121E, T54V 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 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 20% (W/V) PEG 6000, 0.1 M SODIUM ACETATE, 5% ETHANOL, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→40 Å / Num. obs: 77347 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.17 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.55 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT / Resolution: 1.2→40 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.896 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.044 / 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: 18.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.23 Å / Total num. of bins used: 20
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