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Yorodumi- PDB-8w02: Q108K:K40L:T51V:T53S:R58W mutant of hCRBPII bound to synthetic fl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w02 | ||||||
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Title | Q108K:K40L:T51V:T53S:R58W mutant of hCRBPII bound to synthetic fluorophore TD-1V | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | RETINOL BINDING PROTEIN / human cellular retinol binding protein II / hCRBPII / TD-1V / engineered protein / fluorescent protein | ||||||
Function / homology | Function and homology information vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å | ||||||
Authors | Ghanbarpour, A. / Geiger, J.H. / Borhan, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Regulation of Emission via a Protein-Bound Fluorophore Authors: Santos, E.M. / Chandra, I. / Assar, Z. / Sheng, W. / Ghanbarpour, A. / Bingham, C.R. / 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 | 8w02.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w02.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8w02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w02_validation.pdf.gz | 680.3 KB | Display | wwPDB validaton report |
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Full document | 8w02_full_validation.pdf.gz | 683.1 KB | Display | |
Data in XML | 8w02_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 8w02_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/8w02 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w02 | HTTPS FTP |
-Related structure data
Related structure data | 8vzxC 8vzyC 8vzzC 8w00C 4qynS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 15595.499 Da / Num. of mol.: 2 / Mutation: Q108K:K40L:T51V:T53S:R58W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120 #2: Chemical | #3: Chemical | ChemComp-A1AEQ / ( | Mass: 271.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NOS #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, PEG 4000, sodium acetate / PH range: 4.0 - 4.8 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.499→27.36 Å / Num. obs: 39448 / % possible obs: 96.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.22 Å2 / CC1/2: 0.882 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/av σ(I): 41.07 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.499→1.553 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.24 / Num. unique obs: 11993 / CC1/2: 0.89 / CC star: 0.97 / Rpim(I) all: 0.281 / Rrim(I) all: 0.555 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4QYN Resolution: 1.499→27.36 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 32.33 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.499→27.36 Å
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Refine LS restraints |
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