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Yorodumi- PDB-1rwt: Crystal Structure of Spinach Major Light-harvesting complex at 2.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rwt | |||||||||
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Title | Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution | |||||||||
Components | Chlorophyll A-B binding protein, chloroplast | |||||||||
Keywords | PHOTOSYNTHESIS / LIGHT-HARVESTING COMPLEX / MEMBRANE PROTEIN / PLANT | |||||||||
Function / homology | Function and homology information plastoglobule / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / metal ion binding Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR in combination with real-space averaging refinement, extension / Resolution: 2.72 Å | |||||||||
Authors | Liu, Z. / Yan, H. / Wang, K. / Kuang, T. / Zhang, J. / Gui, L. / An, X. / Chang, W. | |||||||||
Citation | Journal: Nature / Year: 2004 Title: Crystal structure of spinach major light-harvesting complex at 2.72 A resolution Authors: Liu, Z. / Yan, H. / Wang, K. / Kuang, T. / Zhang, J. / Gui, L. / An, X. / Chang, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rwt.cif.gz | 718.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rwt.ent.gz | 661 KB | Display | PDB format |
PDBx/mmJSON format | 1rwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rwt_validation.pdf.gz | 50.8 MB | Display | wwPDB validaton report |
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Full document | 1rwt_full_validation.pdf.gz | 50.6 MB | Display | |
Data in XML | 1rwt_validation.xml.gz | 199.6 KB | Display | |
Data in CIF | 1rwt_validation.cif.gz | 219.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwt ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwt | 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 on special symmetry positions |
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-Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 25000.330 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Tissue: leaf / References: UniProt: P12333 |
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-Sugars , 2 types, 20 molecules
#2: Sugar | ChemComp-BNG / #8: Sugar | ChemComp-DGD / |
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-Non-polymers , 8 types, 890 molecules
#3: Chemical | ChemComp-NA / | ||||||||||||
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#4: Chemical | ChemComp-LUT / ( #5: Chemical | ChemComp-XAT / ( #6: Chemical | ChemComp-NEX / ( #7: Chemical | ChemComp-LHG / #9: Chemical | ChemComp-CHL / #10: Chemical | ChemComp-CLA / #11: 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: 5.36 Å3/Da / Density % sol: 76.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: Citrate trisodium, beta-nonyl-glucoside, deoxy-bigchap, DGDG, Hepes, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.7→25 Å / Num. all: 211079 / Num. obs: 191660 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.4 | |||||||||||||||
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9188 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIR in combination with real-space averaging refinement, extension Resolution: 2.72→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 557510.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7972 Å2 / ksol: 0.37093 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.72→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.89 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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