+Open data
-Basic information
Entry | Database: PDB / ID: 1ag6 | ||||||
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Title | PLASTOCYANIN FROM SPINACH | ||||||
Components | PLASTOCYANIN | ||||||
Keywords | ELECTRON TRANSPORT / BLUE-COPPER PROTEIN / ELECTRON TRANSFER | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Xue, Y. / Okvist, M. / Young, S. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structure of spinach plastocyanin at 1.7 A resolution. Authors: Xue, Y. / Okvist, M. / Hansson, O. / Young, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ag6.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ag6.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ag6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1ag6 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1ag6 | HTTPS FTP |
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-Related structure data
Related structure data | 1plcS 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: 10478.593 Da / Num. of mol.: 1 / Mutation: G8D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spinacia oleracea (spinach) / Cell line: BL21 / Cellular location: THYLAKOID / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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: 2.57 Å3/Da / Density % sol: 52.19 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.4 / Details: pH 4.4 | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 12009 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 98 |
Reflection | *PLUS Num. obs: 11977 / % possible obs: 99 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 91.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PLC Resolution: 1.6→30 Å / Cross valid method: THROUGHOUT / Details: X-PLOR (BRUNGER) ALSO WAS USED.
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Displacement parameters | Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |