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Open data
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Basic information
Entry | Database: PDB / ID: 4rkn | ||||||
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Title | Wolinella succinogenes octaheme sulfite reductase MccA, form II | ||||||
![]() | MccA | ||||||
![]() | UNKNOWN FUNCTION / multiheme cytochrome c / sulfite reductase / periplasmic | ||||||
Function / homology | ![]() Oxidoreductases; Acting on a sulfur group of donors; With unknown physiological acceptors / oxidoreductase activity, acting on a sulfur group of donors / sulfite reductase activity / hydrogen sulfide biosynthetic process / anaerobic respiration / cuprous ion binding / protein homotrimerization / periplasmic space / heme binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hermann, B. / Kern, M. / La Pietra, L. / Simon, J. / Einsle, O. | ||||||
![]() | ![]() Title: The octahaem MccA is a haem c-copper sulfite reductase. Authors: Hermann, B. / Kern, M. / La Pietra, L. / Simon, J. / Einsle, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 594.7 KB | Display | ![]() |
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PDB format | ![]() | 509.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 12.7 MB | Display | ![]() |
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Full document | ![]() | 12.9 MB | Display | |
Data in XML | ![]() | 118.6 KB | Display | |
Data in CIF | ![]() | 165.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 82087.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: C-terminal double-StrepTag(II) Source: (gene. exp.) ![]() Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W Gene: mcca, WS0379 / Production host: ![]() |
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-Non-polymers , 5 types, 1465 molecules ![](data/chem/img/DTN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/SO3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DTN / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CU / #5: Chemical | ChemComp-SO3 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 15% PEG 3350, 0.1 M CHES/NaOH, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2012 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7389 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.26 Å / Num. all: 176117 / Num. obs: 175765 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 26.761 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.26 Å
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Refine LS restraints |
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