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Open data
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Basic information
Entry | Database: PDB / ID: 1pl4 | ||||||
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Title | Crystal Structure of human MnSOD Y166F mutant | ||||||
![]() | Superoxide dismutase [Mn], mitochondrial | ||||||
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Function / homology | ![]() acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / cellular response to ethanol / superoxide anion generation / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / negative regulation of fat cell differentiation / response to zinc ion / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fan, L. / Tainer, J.A. | ||||||
![]() | ![]() Title: Amino acid substitution at the dimeric interface of human manganese superoxide dismutase Authors: Hearn, A.S. / Fan, L. / Lepock, J.R. / Luba, J.P. / Greenleaf, W.B. / Cabelli, D.E. / Tainer, J.A. / Nick, H.S. / Silverman, D.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
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PDB format | ![]() | 141 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pm9C ![]() 1abm S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Details | The four molecules in the asymmetric unit reveal the biological tetrameric assembly. |
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Components
#1: Protein | Mass: 22217.111 Da / Num. of mol.: 4 / Mutation: Y166F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.75 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 7.6 Details: PEG 3350, potassium phosphate, pH 7.6, VAPOR DIFFUSION, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→30 Å / Num. obs: 123885 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4788 / Rsym value: 0.386 / % possible all: 73 |
Reflection shell | *PLUS % possible obs: 73 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1ABM ![]() 1abm Resolution: 1.47→30 Å / Num. parameters: 27839 / Num. restraintsaints: 25962 Isotropic thermal model: Isotropic but anisotropic on Mn and solvent atoms Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Displacement parameters | Biso mean: 17.5 Å2 | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 6052 / Occupancy sum non hydrogen: 6934 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 96 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |