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Yorodumi- PDB-7w6w: Crystal structure of a mutant Staphylococcus equorum manganese su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w6w | ||||||
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Title | Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase L169W | ||||||
Components | Superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / superoxide dismutase / Staphylococcus equorum | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus equorum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Retnoningrum, D.S. / Yoshida, H. / Artarini, A.A. / Ismaya, W.T. | ||||||
Funding support | Indonesia, 1items
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Citation | Journal: Appl.Biochem.Biotechnol. / Year: 2023 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: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w6w.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w6w.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 7w6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w6w_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 7w6w_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 7w6w_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 7w6w_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6w ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6w | HTTPS FTP |
-Related structure data
Related structure data | 7wnkC 7wnlC 5x2jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23575.078 Da / Num. of mol.: 4 / Mutation: D13R,L169W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus equorum (bacteria) / Gene: AST02_02815 / Plasmid: pJExpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E5TT85, superoxide dismutase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MPD, PEG 1000, PEG 3350, L-Na-Glutamate, Alanine, Glycine, Lysine, Serine, HEPES, MOPS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
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: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→45.51 Å / Num. obs: 58954 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.032 / Rrim(I) all: 0.058 / Net I/σ(I): 14.4 / Num. measured all: 193383 / Scaling rejects: 128 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5x2j Resolution: 1.94→42.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.164 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.174 / 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: 113.17 Å2 / Biso mean: 37.639 Å2 / Biso min: 17.48 Å2
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Refinement step | Cycle: final / Resolution: 1.94→42.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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