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Yorodumi- PDB-2dre: Crystal structure of Water-soluble chlorophyll protein from lepid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dre | ||||||
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Title | Crystal structure of Water-soluble chlorophyll protein from lepidium virginicum at 2.00 angstrom resolution | ||||||
Components | Water-soluble chlorophyll protein | ||||||
Keywords | PLANT PROTEIN / BETA-TREFOIL / TETRAMER / PLANT / LEPIDIUM VIRGINICUM / CHLOROPHYLL / WATER-SOLUBLE CHLOROPHYLL PROTEIN / SINGLET OXYGEN / PHOTOOXIDATION / CHLOROPHYLL CARRIER / KUNITZ (STI) INHIBITORS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lepidium virginicum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Horigome, D. / Satoh, H. / Itoh, N. / Mitsunaga, K. / Oonishi, I. / Nakagawa, A. / Uchida, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein. Authors: Horigome, D. / Satoh, H. / Itoh, N. / Mitsunaga, K. / Oonishi, I. / Nakagawa, A. / Uchida, A. #1: Journal: Plant Cell.Physiol. / Year: 2001 Title: Water-soluble chlorophyll protein in Brassicaceae plants is a stress-induced chlorophyll-binding protein Authors: Satoh, H. / Uchida, A. / Nakayama, K. / Okada, M. #2: Journal: Biochim.Biophys.Acta / Year: 1980 Title: Crystallization of water-soluble chlorophyll-proteins from Lepidium virginicum Authors: Murata, T. / Itoh, R. / Yakushiji, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dre.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dre.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dre_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2dre_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2dre_validation.xml.gz | 41 KB | Display | |
Data in CIF | 2dre_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2dre ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2dre | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19591.527 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-180 / Source method: isolated from a natural source / Source: (natural) Lepidium virginicum (plant) / Tissue: Leaf / References: UniProt: O04797 #2: Chemical | ChemComp-CLA / #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: 2.2 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M SODIUM/POTASSIUM PHOSPHATE, 3.2M AMMONIUM SULFATE, 5% SUCROSE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2003 |
Radiation | Monochromator: TRIANGULAR SI(111) WITH AN ASYMMETRIC ANGLE OF 7.8 DEGREES Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.99 Å / Num. obs: 50390 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.063 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.494 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→28.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1987876.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ALL OF THE FOUR CHLOROPHYLLS IN THE ASYMMETRIC UNIT WERE IDENTIFIED AS CHLOROPHYLL-A.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.55 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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