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Yorodumi- PDB-2jlp: Crystal structure of human extracellular copper-zinc superoxide d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jlp | ||||||
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Title | Crystal structure of human extracellular copper-zinc superoxide dismutase. | ||||||
Components | EXTRACELLULAR SUPEROXIDE DISMUTASE (CU-ZN) | ||||||
Keywords | OXIDOREDUCTASE / GLYCOLISATION / HEPARIN BINDING / HEPARIN-BINDING / OXIDATIVE STRESS / ANTIOXIDANT / GLYCOPROTEIN / METAL-BINDING / CU-ZN / SECRETED / GLYCATION | ||||||
Function / homology | Function and homology information response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / removal of superoxide radicals / Golgi lumen / heparin binding / cellular response to oxidative stress / collagen-containing extracellular matrix / response to hypoxia ...response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / removal of superoxide radicals / Golgi lumen / heparin binding / cellular response to oxidative stress / collagen-containing extracellular matrix / response to hypoxia / copper ion binding / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Antonyuk, S.V. / Strange, R.W. / Marklund, S.L. / Hasnain, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The Structure of Human Extracellular Copper-Zinc Superoxide Dismutase at 1.7 A Resolution: Insights Into Heparin and Collagen Binding. Authors: Antonyuk, S.V. / Strange, R.W. / Marklund, S.L. / Hasnain, S.S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jlp.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jlp.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jlp_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 2jlp_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 2jlp_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2jlp_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/2jlp ftp://data.pdbj.org/pub/pdb/validation_reports/jl/2jlp | HTTPS FTP |
-Related structure data
Related structure data | 2c9vS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24196.838 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: P08294, superoxide dismutase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | ELECTRON DENSITY AND WATER NETWORK IS IN AGREEMENT WITH THR IN POSITION 40 | |
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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: 1.93 Å3/Da / Density % sol: 36.2 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: PEG3350, THIOCYANATE, BIS-TRIS PROPANE PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 22, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28.2 Å / Num. obs: 81056 / % possible obs: 97.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C9V Resolution: 1.7→28.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.546 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.2 Å
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Refine LS restraints |
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