+Open data
-Basic information
Entry | Database: PDB / ID: 3esy | ||||||
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Title | E16KE61K Flavodoxin from Anabaena | ||||||
Components | Flavodoxin | ||||||
Keywords | ELECTRON TRANSPORT / ALPHA and BETA PROTEIN / Flavoprotein / FMN / Transport | ||||||
Function / homology | Function and homology information cellular response to iron ion starvation / electron transport chain / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | Anabaena sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Herguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Goni, G. / Medina, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Flavodoxin: A compromise between efficiency and versatility in the electron transfer from Photosystem I to Ferredoxin-NADP(+) reductase Authors: Goni, G. / Herguedas, B. / Hervas, M. / Peregrina, J.R. / De la Rosa, M.A. / Gomez-Moreno, C. / Navarro, J.A. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3esy.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esy.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 3esy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3esy_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3esy_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3esy_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 3esy_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esy ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esy | HTTPS FTP |
-Related structure data
Related structure data | 3esxC 3eszC 1flvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18847.660 Da / Num. of mol.: 4 / Mutation: E16K, E61K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: PCC 7119 / Plasmid: pTrc99a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P0A3E0 #2: Chemical | ChemComp-FMN / #3: Chemical | #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: 1.98 Å3/Da / Density % sol: 38.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 32% PEG 4000, 0.2-0.3M magnesium chloride, 0.1M Tris/HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Dec 15, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→47.2 Å / Num. all: 24311 / Num. obs: 22468 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.387 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLV Resolution: 2.39→22.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.204 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→22.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.393→2.455 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 37.6871 Å / Origin y: 19.4711 Å / Origin z: 68.8769 Å
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Refinement TLS group |
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