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Yorodumi- PDB-2gj5: Crystal structure of a secondary vitamin D3 binding site of milk ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gj5 | ||||||
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Title | Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin | ||||||
Components | Beta-lactoglobulin | ||||||
Keywords | TRANSPORT PROTEIN / beta-lactoglobulin / vitamin D3 | ||||||
Function / homology | Function and homology information retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Yang, M.C. / Guan, H.H. / Liu, M.Y. / Yang, J.M. / Chen, W.L. / Chen, C.J. / Mao, S.J. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin. Authors: Yang, M.C. / Guan, H.H. / Liu, M.Y. / Lin, Y.H. / Yang, J.M. / Chen, W.L. / Chen, C.J. / Mao, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gj5.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gj5.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/2gj5 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/2gj5 | HTTPS FTP |
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-Related structure data
Related structure data | 2blgS 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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754 | ||
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#2: Chemical | #3: 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: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 1.4M tri-sodium citrate dehydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2005 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. all: 7671 / Num. obs: 7671 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.038 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BLG Resolution: 2.4→15 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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