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- PDB-5ch7: Crystal structure of the perchlorate reductase PcrAB - Phe164 gat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ch7 | ||||||
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Title | Crystal structure of the perchlorate reductase PcrAB - Phe164 gate switch intermediate - from Azospira suillum PS | ||||||
![]() | (DMSO reductase family type II enzyme, ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / electron-shuttling protein | ||||||
Function / homology | ![]() oxidoreductase complex / molybdopterin cofactor binding / anaerobic respiration / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / oxidoreductase activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsai, C.-L. / Tainer, J.A. | ||||||
![]() | ![]() Title: Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues. Authors: Youngblut, M.D. / Tsai, C.L. / Clark, I.C. / Carlson, H.K. / Maglaqui, A.P. / Gau-Pan, P.S. / Redford, S.A. / Wong, A. / Tainer, J.A. / Coates, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 798.5 KB | Display | ![]() |
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PDB format | ![]() | 643.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | Dimer confirmed by gel filtration and SAXS |
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Components
-DMSO reductase family type II enzyme, ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 102069.859 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-33 / DSM 13638 / PS / References: UniProt: G8QM55 #2: Protein | Mass: 37067.809 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC BAA-33 / DSM 13638 / PS / References: UniProt: G8QM54 |
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-Non-polymers , 12 types, 2030 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/MD1.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/MD1.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-NA / #9: Chemical | #10: Chemical | ChemComp-GOL / | #11: Chemical | ChemComp-SO3 / #12: Chemical | #13: Chemical | ChemComp-ACT / | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % / Description: Rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 / Details: 20% PEG6K, 0.1 M Tris pH 8.5 anaerobically / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.38 Å / Num. obs: 228466 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PcrAB_4YDD Resolution: 2.2→48.38 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.38 Å
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Refine LS restraints |
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LS refinement shell |
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