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Yorodumi- PDB-3f8a: Crystal Structure of the R132K:R111L:L121E:R59W Mutant of Cellula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f8a | ||||||
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Title | Crystal Structure of the R132K:R111L:L121E:R59W Mutant of Cellular Retinoic Acid-Binding Protein Type II Complexed with C15-aldehyde (a retinal analog) at 1.95 Angstrom resolution. | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / CRABPII / retinal / protonated schiff base / C15-aldehyde / retinoic acid / retinoid / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Jia, X. / Geiger, J.H. | ||||||
Citation | Journal: Chempluschem / Year: 2012 Title: Probing Wavelength Regulation with an Engineered Rhodopsin Mimic and a C15-Retinal Analogue Authors: Lee, K.S. / Berbasova, T. / Vasileiou, C. / Jia, X. / Wang, W. / Choi, Y. / Nossoni, F. / Geiger, J.H. / Borhan, B. #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 | 3f8a.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f8a.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 3f8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f8a_validation.pdf.gz | 847.6 KB | Display | wwPDB validaton report |
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Full document | 3f8a_full_validation.pdf.gz | 850.3 KB | Display | |
Data in XML | 3f8a_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3f8a_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8a ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8a | HTTPS FTP |
-Related structure data
Related structure data | 2g7bS 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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Unit cell |
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-Components
#1: Protein | Mass: 15554.726 Da / Num. of mol.: 1 / Mutation: R132K, R111L, L121E, R59W 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 |
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#2: Chemical | ChemComp-B3P / |
#3: Chemical | ChemComp-LSR / |
#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: 3.3 Å3/Da / Density % sol: 62.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M bis-tris-propane, 30% PEG400, pH 7.5, 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-D / Wavelength: 0.97869 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 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: 1.95→50 Å / Num. obs: 14776 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.6 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G7B Resolution: 1.95→28.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.378 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.152 / 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: 27.887 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→28.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.003 Å / Total num. of bins used: 20
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