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Yorodumi- PDB-3fou: Low pH structure of the Rieske protein from Thermus thermophilus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fou | ||||||
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Title | Low pH structure of the Rieske protein from Thermus thermophilus at 2.1 A | ||||||
Components | Quinol-cytochrome c reductase, Rieske iron-sulfur subunit | ||||||
Keywords | ELECTRON TRANSPORT / Rieske protein / Pr / [2Fe-2S] | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hunsicker-Wang, L.M. / Taylor, A.B. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Effects of pH on the Rieske Protein from Thermus thermophilus: A Spectroscopic and Structural Analysis Authors: Konkle, M.E. / Muellner, S.K. / Schwander, A.L. / Dicus, M.M. / Pokhrel, R. / Britt, R.D. / Taylor, A.B. / Hunsicker-Wang, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fou.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fou.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fou_validation.pdf.gz | 458.8 KB | Display | wwPDB validaton report |
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Full document | 3fou_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 3fou_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3fou_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/3fou ftp://data.pdbj.org/pub/pdb/validation_reports/fo/3fou | HTTPS FTP |
-Related structure data
Related structure data | 1nykS 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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Details | biological unit is the asymmetric unit |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 16432.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1931 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SGZ9 |
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-Non-polymers , 5 types, 126 molecules
#2: Chemical | #3: Chemical | ChemComp-PR / #4: Chemical | #5: Chemical | #6: 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: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.21 Details: PEG 8000, Na Cacodylate, Calcium acetate, Pr(acetate)3, pH 6.21, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 11, 2008 / Details: Mirrors |
Radiation | Monochromator: Confocal multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→58.8 Å / Num. obs: 23456 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rsym value: 0.088 |
Reflection shell | Resolution: 2.099→2.154 Å / Redundancy: 4.4 % / Num. unique all: 2311 / Rsym value: 0.529 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Protein A of 1NYK Resolution: 2.1→58.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.985 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.176 / 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: 37.758 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→58.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.099→2.154 Å / Total num. of bins used: 20
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