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- PDB-7wnl: Crystal structure of a mutant Staphylococcus equorum manganese su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wnl | ||||||
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Title | Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121Y | ||||||
![]() | Superoxide dismutase | ||||||
![]() | OXIDOREDUCTASE / superoxide dismutase / Staphylococcus equorum | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Retnoningrum, D.S. / Yoshida, H. / Artarini, A.A. / Ismaya, W.T. | ||||||
Funding support | Indonesia, 1items
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![]() | ![]() Title: Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Authors: Retnoningrum, D.S. / Yoshida, H. / Pajatiwi, I. / Muliadi, R. / Utami, R.A. / Artarini, A. / Ismaya, W.T. #1: ![]() Title: The first crystal structure of manganese superoxide dismutase from the genus Staphylococcus. Authors: Retnoningrum, D.S. / Yoshida, H. / Arumsari, S. / Kamitori, S. / Ismaya, W.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 384.7 KB | Display | ![]() |
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PDB format | ![]() | 313.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482 KB | Display | ![]() |
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Full document | ![]() | 485.7 KB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 64.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w6wC ![]() 7wnkC ![]() 5x2jS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 23622.139 Da / Num. of mol.: 4 / Mutation: D13R, K38R, A121Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1176 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-AZI / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium fluoride, sodium bromide, sodium iodide, imidazole, MES, PEG MME 500, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.51→45.93 Å / Num. obs: 144687 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.047 / Rrim(I) all: 0.115 / Net I/σ(I): 10.7 / Num. measured all: 873802 / Scaling rejects: 74 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5x2j Resolution: 1.51→44.79 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.911 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.49 Å2 / Biso mean: 19.993 Å2 / Biso min: 8.08 Å2
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Refinement step | Cycle: final / Resolution: 1.51→44.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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