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Yorodumi- PDB-3ah7: Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ah7 | ||||||
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Title | Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004 | ||||||
Components | [2Fe-2S]ferredoxin | ||||||
Keywords | METAL BINDING PROTEIN / ferredoxin / [2Fe-2S] cluster / iron-sulfur cluster biosynthesis / Pseudomonas | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kumasaka, T. / Shimizu, N. / Ohmori, D. / Iwasaki, T. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004 Authors: Iwasaki, T. / Kappl, R. / Bracic, G. / Shimizu, N. / Ohmori, D. / Kumasaka, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004 Authors: Iwasaki, T. / Ohmori, D. / Shimizu, N. / Kumasaka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ah7.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ah7.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ah7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ah7 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ah7 | HTTPS FTP |
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-Related structure data
Related structure data | 1i7hS 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 on special symmetry positions |
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-Components
#1: Protein | [ Mass: 12517.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: JCM 20004 / Gene: fdxB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q76CS9 |
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#2: Chemical | ChemComp-FES / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-CL / |
#5: 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: 3.23 Å3/Da / Density % sol: 61.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M trisodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2007 |
Radiation | Monochromator: Rotated-inclined double-crystal monochromator (Si(111)), K-B mirror (Rh coated) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→75.81 Å / Num. obs: 13390 / % possible obs: 98.6 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9 % / Rmerge(I) obs: 0.35 / Num. unique all: 1285 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1i7h Resolution: 1.9→37.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.452 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / 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: 18.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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