+Open data
-Basic information
Entry | Database: PDB / ID: 4blc | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF ORTHORHOMBIC CRYSTALS OF BEEF LIVER CATALASE | ||||||
Components | PROTEIN (CATALASE) | ||||||
Keywords | OXIDOREDUCTASE / LATTICE CONTACT / HEME PROTEIN | ||||||
Function / homology | Function and homology information Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide ...Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ko, T.P. / Day, J. / Malkin, A. / McPherson, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of orthorhombic crystals of beef liver catalase. Authors: Ko, T.P. / Day, J. / Malkin, A.J. / McPherson, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4blc.cif.gz | 414.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4blc.ent.gz | 340.1 KB | Display | PDB format |
PDBx/mmJSON format | 4blc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4blc ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4blc | HTTPS FTP |
---|
-Related structure data
Related structure data | 7catS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57664.465 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA CHEMICAL CO., ST.LOUIS, MO / Source: (natural) Bos taurus (cattle) / Organ: LIVER / References: UniProt: P00432, catalase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-NDP / #4: Water | ChemComp-HOH / | Nonpolymer details | THE FE ATOM IS BOUND TO TYR 357 OH | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 6.5 Details: VAPOR DIFFUSION AGAINST 10% N-PROPANOL, AND 0.1 M NA-PO4 BUFFER PH 6.2 TO 6.8 DROP SET UP 15 UL OF 40 MG/ML PROTEIN PLUS 5 UL 1% NACL PLUS 5 UL RESERVOIR., pH 6.5, vapor diffusion PH range: 6.2-6.8 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 290 K / Method: vapor diffusion / PH range low: 6.8 / PH range high: 6.2 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Monochromator: SUPPER GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 128019 / % possible obs: 88.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.226 / % possible all: 26.9 |
Reflection | *PLUS Num. measured all: 603135 |
Reflection shell | *PLUS % possible obs: 26.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7CAT Resolution: 2.3→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|