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Yorodumi- PDB-3pl9: Crystal structure of spinach minor light-harvesting complex CP29 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pl9 | ||||||||||||
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Title | Crystal structure of spinach minor light-harvesting complex CP29 at 2.80 angstrom resolution | ||||||||||||
Components | Chlorophyll A-B binding proteinLight-harvesting complexes of green plants | ||||||||||||
Keywords | PHOTOSYNTHESIS / CP29 / Chlorophyll A-B binding protein / light-harvesting complex / membrane protein / plant / chloroplast / thylakoid / photosystem II | ||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / phosphoprotein binding Similarity search - Function | ||||||||||||
Biological species | Spinacia oleracea (spinach) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å | ||||||||||||
Authors | Pan, X.W. / Li, M. / Wan, T. / Wang, L.F. / Jia, C.J. / Hou, Z.Q. / Zhao, X.L. / Zhang, J.P. / Chang, W.R. | ||||||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Structural insights into energy regulation of light-harvesting complex CP29 from spinach. Authors: Pan, X. / Li, M. / Wan, T. / Wang, L. / Jia, C. / Hou, Z. / Zhao, X. / Zhang, J. / Chang, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pl9.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pl9.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/3pl9 ftp://data.pdbj.org/pub/pdb/validation_reports/pl/3pl9 | HTTPS FTP |
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-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
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 26735.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: F2Z293*PLUS |
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#8: Sugar |
-Non-polymers , 7 types, 96 molecules
#2: Chemical | ChemComp-CLA / #3: Chemical | ChemComp-CHL / #4: Chemical | ChemComp-LUT / ( | #5: Chemical | ChemComp-XAT / ( | #6: Chemical | ChemComp-NEX / ( | #7: Chemical | ChemComp-G3P / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
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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: 5.44 Å3/Da / Density % sol: 77.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM MES, pH 6.5, 2.80% (w/v) HTG, 19% (w/v) PEG 1000, 0.1M sodium chloride, 0.19M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99985 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 15, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 15959 / Num. obs: 14714 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 5.6 / Num. unique all: 627 / % possible all: 40.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.8→42.56 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 3581533.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4318 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→42.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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