+Open data
-Basic information
Entry | Database: PDB / ID: 1qqw | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ERYTHROCYTE CATALASE | ||||||
Components | CATALASE | ||||||
Keywords | OXIDOREDUCTASE / HEME PROTEIN / LATTICE CONTACT / WATER / NO NADP | ||||||
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 L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity ...response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity / catalase / UV protection / response to fatty acid / response to vitamin A / catalase activity / 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 / peroxisome / response to estradiol / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.75 Å | ||||||
Authors | Ko, T.P. / Safo, M.K. / Musayev, F.N. / Wang, C. / Wu, S.H. / Abraham, D.J. | ||||||
Citation | 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 | 1qqw.cif.gz | 393.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qqw.ent.gz | 322.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qqw_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1qqw_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1qqw_validation.xml.gz | 48.9 KB | Display | |
Data in CIF | 1qqw_validation.cif.gz | 70.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqw ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqw | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 59836.996 Da / Num. of mol.: 4 / 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: 2.92 Å3/Da / Density % sol: 57.86 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: PROTEIN SOLUTION: 8MG/ML PROTEIN, 50MM KCL, 1MM 2-MERCAPTOETHANOL, 0.2MM EDTA, 20MM NAOAC PH 5.2; RESERVOIR: 6-7% PEG-20000, 0.1 M MES PH 6.7; DROPS WERE SET UP BY MIXING EQUAL VOLUMES OF ...Details: PROTEIN SOLUTION: 8MG/ML PROTEIN, 50MM KCL, 1MM 2-MERCAPTOETHANOL, 0.2MM EDTA, 20MM NAOAC PH 5.2; RESERVOIR: 6-7% PEG-20000, 0.1 M MES PH 6.7; DROPS WERE SET UP BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION AND RESERVOIR., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 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 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→240 Å / Num. all: 75169 / Num. obs: 64674 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 2.9 |
Reflection shell | Resolution: 2.73→2.82 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.354 / % possible all: 67 |
Reflection | *PLUS Num. measured all: 131236 / Rmerge(I) obs: 0.109 |
Reflection shell | *PLUS % possible obs: 67 % / Num. unique obs: 4606 / Num. measured obs: 7325 |
-Processing
Software |
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Refinement | Resolution: 2.75→40 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER / Details: NCS RESTRAINTS WERE APPLIED
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Refinement step | Cycle: LAST / Resolution: 2.75→40 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 8 % / Rfactor all: 0.239 / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 2.85 Å / Rfactor Rfree: 0.432 / Num. reflection Rfree: 2417 / Rfactor Rwork: 0.299 / Num. reflection obs: 4498 |