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- PDB-6m30: 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: 6m30 | ||||||
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Title | Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase N73F | ||||||
![]() | Superoxide dismutase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Retnoningrum, D.S. / Yoshida, H. / Razani, M.D. / Meidianto, V.F. / Hartanto, A. / Artarini, A. / Ismaya, W.T. | ||||||
![]() | ![]() Title: Unprecedented Role of The N73-F124 Pair in The Staphylococcus equorum MnSOD Activity. Authors: Retnoningrum, D.S. / Yoshida, H. / Razani, M.D. / Meidianto, V.F. / Hartanto, 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 | ![]() | 504.1 KB | Display | ![]() |
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PDB format | ![]() | 414.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5x2jS S: Starting model for refinement |
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Similar 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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Components
#1: Protein | ![]() Mass: 23535.098 Da / Num. of mol.: 6 / Mutation: D13R, N73F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ammonium sulfate, Bis-Tris, Pentaerythritol ethoxylate |
-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: Nov 9, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.74→46.28 Å / Num. obs: 137152 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Net I/σ(I): 8.4 / Num. measured all: 469453 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5X2J Resolution: 1.74→44.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.361 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.106 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.34 Å2 / Biso mean: 24.268 Å2 / Biso min: 11.23 Å2
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Refinement step | Cycle: final / Resolution: 1.74→44.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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