+Open data
-Basic information
Entry | Database: PDB / ID: 3km1 | ||||||
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Title | ZINC-Reconstituted TOMATO CHLOROPLAST SUPEROXIDE DISMUTASE | ||||||
Components | Superoxide dismutase [Cu-Zn], chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / TOMATO CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / CHLOROPLAST / DISULFIDE BOND / TRANSIT PEPTIDE | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / chloroplast / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Galaleldeen, A. / Taylor, A.B. / Thomas, S.T. / Hart, P.J. | ||||||
Citation | Journal: To be Published Title: Biophysical properties of tomato chloroplast sod Authors: Galaleldeen, A. / Taylor, A.B. / Thomas, S.T. / Jart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3km1.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3km1.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 3km1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3km1_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 3km1_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 3km1_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3km1_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/3km1 ftp://data.pdbj.org/pub/pdb/validation_reports/km/3km1 | HTTPS FTP |
-Related structure data
Related structure data | 3km2C 3mkgC 1azvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15644.372 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: SODCP.2 / Plasmid: PAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14831, superoxide dismutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 2M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 22, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17370 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4 / Num. unique all: 1691 / Rsym value: 0.435 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AZV Resolution: 2→40.943 Å / SU ML: 0.24 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.943 Å
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Refine LS restraints |
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LS refinement shell |
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