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Yorodumi- PDB-3fel: Crystal structure of the R132K:R111L:T54E mutant of cellular reti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fel | ||||||
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Title | Crystal structure of the R132K:R111L:T54E mutant of cellular retinoic acid-binding protein II at 1.85 angstrom resolution | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / CRABPII / 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: 1.85 Å | ||||||
Authors | Jia, X. / Geiger, J.H. | ||||||
Citation | Journal: To be Published Title: Crystal structures of apo cellular retinoic acid-binding protein II mutants: Structural integrity investigated through multiple site mutations Authors: Jia, X. / Lee, K.S. / Vasileiou, C. / Borhan, B. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fel.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fel.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fel_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3fel_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3fel_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3fel_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/3fel ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3fel | HTTPS FTP |
-Related structure data
Related structure data | 3fa7C 3fa8C 3fa9C 3fekC 3fenC 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-KL-T54E / 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: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M BTP, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2007 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→53.2 Å / Num. obs: 18943 / % possible obs: 84.5 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.4 / Num. unique all: 959 / % possible all: 43.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G7B Resolution: 1.85→35.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.503 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.183 / 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: 24.122 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→35.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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