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Yorodumi- PDB-3f9d: Crystal structure of the R132K:R111L:T54E mutant of cellular reti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f9d | ||||||
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Title | Crystal structure of the R132K:R111L:T54E mutant of cellular retinoic acid-binding protein II complexed with C15-aldehyde (a retinal analog) at 2.00 angstrom resolution | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / CRABPII / retinal / protonated Schiff base / PSB / C15-aldehyde / retinoic acid / retinoid / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Jia, X. / Geiger, J.H. | ||||||
Citation | Journal: To be Published Title: Two distinctive orientations of binding determined by a single mutation in the CRABPII mutant-C15-aldehyde complexes Authors: Jia, X. / Lee, K.S. / Vasileiou, C. / Borhan, B. / Geiger, J.H. #1: Journal: To be Published Title: Protein engineering: wavelength regulation mechanism investigated in a rhodopsin mimic Authors: Lee, K.S. / Jia, X. / Vasileiou, C. / Geiger, J.H. / Borhan, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f9d.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f9d.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 3f9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/3f9d ftp://data.pdbj.org/pub/pdb/validation_reports/f9/3f9d | HTTPS FTP |
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-Related structure data
Related structure data | 3cr6C 3fa6C 2g7bS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 15537.763 Da / Num. of mol.: 2 / Mutation: R132K, R111L, T54E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: CRABPII-pET17b-KLE-R59W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29373 #2: Chemical | #3: 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: 3.75 Å3/Da / Density % sol: 67.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.1M sodium acetate, 18% PEG6000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97869 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2007 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→75.8 Å / Num. obs: 38649 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 16.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 56.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 12 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G7B Resolution: 2→43.75 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.508 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.136 / 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: 22.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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