+Open data
-Basic information
Entry | Database: PDB / ID: 2e4p | |||||||||
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Title | Crystal structure of BphA3 (oxidized 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: 2 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: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102 Authors: Senda, M. / Kimura, S. / Kishigami, 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 | 2e4p.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e4p.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 2e4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/2e4p ftp://data.pdbj.org/pub/pdb/validation_reports/e4/2e4p | HTTPS FTP |
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-Related structure data
Related structure data | 2e4qC 2gqwC 2gr0C 2yvfC 2yvgC 2yvjC 1fqtS 2gt0 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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1 |
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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: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose / | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.55M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 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: 2→17 Å / Num. obs: 16179 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.56 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.92 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.32 / Num. unique all: 4024 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FQT Resolution: 2→16.65 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.781 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.739 Å2
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Refinement step | Cycle: LAST / Resolution: 2→16.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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