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Yorodumi- PDB-6giw: Water-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6giw | |||||||||
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Title | Water-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum (Mutation L91P) with Chlorophyll-a | |||||||||
Components | Water-soluble chlorophyll protein | |||||||||
Keywords | PLANT PROTEIN / Tetramer / Plant / Lepidium virginicum / Chlorophyll / Water-soluble Chlorophyll Protein / Photooxidation / Chlorophyll Carrier | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Lepidium virginicum (plant) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Palm, D.M. / Agostini, A. / Averesch, V. / Girr, P. / Werwie, M. / Takahashi, S. / Satoh, H. / Jaenicke, E. / Paulsen, H. | |||||||||
Citation | Journal: Nat Plants / Year: 2018 Title: Chlorophyll a/b binding-specificity in water-soluble chlorophyll protein. Authors: Palm, D.M. / Agostini, A. / Averesch, V. / Girr, P. / Werwie, M. / Takahashi, S. / Satoh, H. / Jaenicke, E. / Paulsen, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6giw.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6giw.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 6giw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6giw_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6giw_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6giw_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 6giw_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/6giw ftp://data.pdbj.org/pub/pdb/validation_reports/gi/6giw | HTTPS FTP |
-Related structure data
Related structure data | 6gixC 2dreS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 19575.484 Da / Num. of mol.: 4 / Mutation: L91P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lepidium virginicum (plant) / Tissue: Leaf / Gene: WSCP1 / Production host: Escherichia coli BL21 (bacteria) / 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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Na/K Phosphate, 3.2M Ammonium sulfate, 5% Sucrose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 5, 2017 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.73 Å / Num. obs: 18323 / % possible obs: 99.1 % / Redundancy: 8.1 % / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 3.08 / Num. unique obs: 1341 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DRE Resolution: 2.8→19.73 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.856 / SU B: 17.163 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.452
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.575 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→19.73 Å
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Refine LS restraints |
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