+Open data
-Basic information
Entry | Database: PDB / ID: 1a70 | ||||||
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Title | SPINACH FERREDOXIN | ||||||
Components | FERREDOXIN | ||||||
Keywords | IRON-SULFUR PROTEIN / PHOTOSYNTHESIS / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information chloroplast / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Binda, C. / Coda, A. / Mattevi, A. / Aliverti, A. / Zanetti, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution. Authors: Binda, C. / Coda, A. / Aliverti, A. / Zanetti, G. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a70.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a70.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a70_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 1a70_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 1a70_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1a70_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a70 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a70 | HTTPS FTP |
-Related structure data
Related structure data | 1frrS 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
#1: Protein | Mass: 10488.470 Da / Num. of mol.: 1 / Mutation: E92K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spinacia oleracea (spinach) / Production host: Escherichia coli (E. coli) / References: UniProt: P00221 |
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#2: Chemical | ChemComp-FES / |
#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: 1.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 2.6M AMMONIUM SULPHATE IN 50MM PHOSPHATE BUFFER, PH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.7 Å / Num. obs: 11755 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 5.1 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.112 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2 / Rsym value: 0.305 / % possible all: 68 |
Reflection | *PLUS Num. measured all: 35600 |
Reflection shell | *PLUS % possible obs: 68 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FRR Resolution: 1.7→100 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: A POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→100 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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