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Yorodumi- PDB-1oow: The crystal structure of the spinach plastocyanin double mutant G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oow | ||||||
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Title | The crystal structure of the spinach plastocyanin double mutant G8D/L12E gives insight into its low reactivity towards photosystem 1 and cytochrome f | ||||||
Components | Plastocyanin, chloroplast | ||||||
Keywords | ELECTRON TRANSPORT / MEMBRANE / CUPREDOXIN / BETA SANDWICH | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Jansson, H. / Okvist, M. / Jacobson, F. / Ejdeback, M. / Hansson, O. / Sjolin, L. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2003 Title: The crystal structure of the spinach plastocyanin double mutant G8D/L12E gives insight into its low reactivity towards photosystem 1 and cytochrome f. Authors: Jansson, H. / Okvist, M. / Jacobson, F. / Ejdeback, M. / Hansson, O. / Sjolin, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oow.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oow.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 1oow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/1oow ftp://data.pdbj.org/pub/pdb/validation_reports/oo/1oow | HTTPS FTP |
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-Related structure data
Related structure data | 1ag6S 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10494.549 Da / Num. of mol.: 1 / Mutation: G8D, L12E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: PETE / Plasmid: pUG101tr / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: P00289 |
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#2: Chemical | ChemComp-CU / |
#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: 2.32 Å3/Da / Density % sol: 46.6 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 32% PEG 3350, 0.25M MgCl2, 0.1M Na-ascorbate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.991 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 13, 2001 |
Radiation | Monochromator: FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.28 Å / Num. all: 6938 / Num. obs: 6400 / % possible obs: 91 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.88 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 7.06 / Num. unique all: 860 / % possible all: 91.6 |
Reflection | *PLUS Lowest resolution: 19.3 Å / Num. all: 6936 / % possible obs: 98.6 % / Num. measured all: 75874 / Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AG6 Resolution: 2→19.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.166 / SU ML: 0.115 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.337 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.055 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 19.3 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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