+Open data
-Basic information
Entry | Database: PDB / ID: 2e4q | ||||||
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Title | Crystal structure of BphA3 (reduced form) | ||||||
Components | Biphenyl dioxygenase ferredoxin subunit | ||||||
Keywords | ELECTRON TRANSPORT / Rieske type [2Fe-2S]cluster | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Senda, M. / Kishigami, S. / Kimura, S. / Ishida, T. / Fukuda, M. / Senda, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin Authors: Senda, M. / Kishigami, S. / Kimura, S. / Fukuda, M. / Ishida, T. / Senda, T. #1: Journal: To be Published Title: Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe-2S] ferredoxin derived from Pseudomonas sp.strain KKS102 Authors: Senda, M. / Kishigami, S. / Kimura, S. / Senda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e4q.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e4q.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 2e4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/2e4q ftp://data.pdbj.org/pub/pdb/validation_reports/e4/2e4q | HTTPS FTP |
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-Related structure data
Related structure data | 2e4pSC 2gqwC 2gr0C 2yvfC 2yvgC 2yvjC 2gt0 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11926.499 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: strain KKS102 / Plasmid: pCA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52440 #2: Chemical | #3: 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: 2.57 Å3/Da / Density % sol: 52.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.8M ammonium sulfate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.4 Å / Num. all: 24101 / Num. obs: 23884 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.55 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.77 / Num. unique all: 2305 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E4P Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.603 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.13 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.216 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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