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Yorodumi- PDB-1jxg: The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jxg | ||||||
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Title | The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge | ||||||
Components | PLASTOCYANIN A | ||||||
Keywords | PHOTOSYNTHESIS / BETA BARREL | ||||||
Function / homology | Function and homology information electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | Populus nigra (black poplar) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Milani, M. / Andolfi, L. / Cannistraro, S. / Verbeet, M.P. / Bolognesi, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: The 1.6 A resolution crystal structure of a mutant plastocyanin bearing a 21-25 engineered disulfide bridge. Authors: Milani, M. / Andolfi, L. / Cannistraro, S. / Verbeet, M.P. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxg.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxg.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxg ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxg | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10588.816 Da / Num. of mol.: 2 / Mutation: I21C, E25C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus nigra (black poplar) / Variant: ITALICA / Production host: Escherichia coli (E. coli) / References: UniProt: P00299 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.11 Å3/Da / Density % sol: 41.73 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||
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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 29, 2000 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35 Å / Num. all: 25069 / Num. obs: 24587 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 4 / Num. unique all: 862 / % possible all: 71.6 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. obs: 25069 / Num. measured all: 135535 |
Reflection shell | *PLUS % possible obs: 71.6 % / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PLC Resolution: 1.6→41 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→41 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.145 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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