+Open data
-Basic information
Entry | Database: PDB / ID: 1f4j | ||||||
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Title | STRUCTURE OF TETRAGONAL CRYSTALS OF HUMAN ERYTHROCYTE CATALASE | ||||||
Components | CATALASE | ||||||
Keywords | OXIDOREDUCTASE / heme protein / no bound NADPH | ||||||
Function / homology | Function and homology information response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to L-ascorbic acid / catalase ...response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to L-ascorbic acid / catalase / UV protection / response to fatty acid / response to light intensity / catalase activity / response to vitamin A / peroxisomal membrane / ureteric bud development / triglyceride metabolic process / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of cell division / response to vitamin E / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / aerobic respiration / cholesterol metabolic process / response to activity / response to reactive oxygen species / hydrogen peroxide catabolic process / Peroxisomal protein import / response to lead ion / response to insulin / response to hydrogen peroxide / cellular response to growth factor stimulus / osteoblast differentiation / response to estradiol / peroxisome / NADP binding / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / response to xenobiotic stimulus / intracellular membrane-bounded organelle / focal adhesion / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Safo, M.K. / Musayev, F.N. / Wu, S.H. / Abraham, D.J. / Ko, T.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of tetragonal crystals of human erythrocyte catalase. Authors: Safo, M.K. / Musayev, F.N. / Wu, S.H. / Abraham, D.J. / Ko, T.P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of Human Erythrocyte Catalase Authors: Ko, T.P. / Safo, M.K. / Musayev, F.N. / Di Salvo, M.L. / Wang, C. / Wu, S.H. / Abraham, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f4j.cif.gz | 410.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f4j.ent.gz | 336.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/1f4j ftp://data.pdbj.org/pub/pdb/validation_reports/f4/1f4j | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | Tetramer of identical subunits A, B, C and D. Assembled with a 222 point-group symmetry |
-Components
#1: Protein | Mass: 59836.996 Da / Num. of mol.: 4 / Fragment: INTACT BUT LACKS THE FIRST AND LAST EXONS / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / Tissue: BLOOD / References: UniProt: P04040, catalase #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | |
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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: 3.13 Å3/Da / Density % sol: 60.68 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: potassium sodium tartrate, HEPES, sodium acetate, potassium chloride, 2-mercaptoethanol, EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.7 Details: Ko, T.P., (2000) Acta Crystallogr., Sect.D, 56, 241. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→204 Å / Num. all: 116954 / Num. obs: 107950 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.249 / Num. unique all: 10206 / % possible all: 76.4 |
Reflection | *PLUS Lowest resolution: 144 Å / Num. measured all: 337583 |
Reflection shell | *PLUS % possible obs: 76.4 % / Num. unique obs: 10206 / Num. measured obs: 23586 / Mean I/σ(I) obs: 1.66 |
-Processing
Software |
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Refinement | Resolution: 2.4→204 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Used noncrystallographic symmetry restraints but released in final cycles of refinement.
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Refinement step | Cycle: LAST / Resolution: 2.4→204 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 144 Å / σ(F): 0 / Rfactor obs: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.406 / Rfactor obs: 0.384 |