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Yorodumi- PDB-4id8: The crystal structure of a [3Fe-4S] ferredoxin associated with CY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4id8 | ||||||
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Title | The crystal structure of a [3Fe-4S] ferredoxin associated with CYP194A4 from R. palustris HaA2 | ||||||
Components | Putative ferredoxin | ||||||
Keywords | ELECTRON TRANSPORT / 4Fe-4S single cluster domain | ||||||
Function / homology | 4Fe-4S single cluster domain / Alpha-Beta Plaits - #20 / 3 iron, 4 sulfur cluster binding / Alpha-Beta Plaits / 2-Layer Sandwich / metal ion binding / Alpha Beta / FE3-S4 CLUSTER / Putative ferredoxin Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Zhou, W.H. / Zhang, T. / Zhang, A.L. / Bell, S.G. / Wong, L.-L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The structure of a novel electron-transfer ferredoxin from Rhodopseudomonas palustris HaA2 which contains a histidine residue in its iron-sulfur cluster-binding motif. Authors: Zhang, T. / Zhang, A. / Bell, S.G. / Wong, L.L. / Zhou, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4id8.cif.gz | 26.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4id8.ent.gz | 15.8 KB | Display | PDB format |
PDBx/mmJSON format | 4id8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4id8_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 4id8_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 4id8_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 4id8_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/4id8 ftp://data.pdbj.org/pub/pdb/validation_reports/id/4id8 | HTTPS FTP |
-Related structure data
Related structure data | 4ov1C 2z8qS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7592.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: HaA2 / Gene: RPB_3630 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2ITY5 |
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#2: Chemical | ChemComp-F3S / |
#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: 1.87 Å3/Da / Density % sol: 34.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.3 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5, 2.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 25, 2012 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 3425 / Num. obs: 3298 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.086 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 7.9 / Num. unique all: 323 / Rsym value: 0.133 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8Q Resolution: 2.15→45.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.385 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.307 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 27.635 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→45.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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