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Yorodumi- PDB-3e4w: Crystal structure of a 33kDa catalase-related protein from Mycoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e4w | ||||||
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Title | Crystal structure of a 33kDa catalase-related protein from Mycobacterium avium subsp. paratuberculosis. P2(1)2(1)2(1) crystal form. | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / heme enzyme / catalase / peroxidase | ||||||
Function / homology | Function and homology information catalase activity / regulation of reactive oxygen species metabolic process / hydrogen peroxide metabolic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / hydrogen peroxide catabolic process / peroxidase activity / response to hydrogen peroxide / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium avium subsp. paratuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pakhomova, S. / Newcomer, M.E. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: The structure and peroxidase activity of a 33-kDa catalase-related protein from Mycobacterium avium ssp. paratuberculosis. Authors: Pakhomova, S. / Gao, B. / Boeglin, W.E. / Brash, A.R. / Newcomer, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e4w.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e4w.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3e4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e4w_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3e4w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3e4w_validation.xml.gz | 29 KB | Display | |
Data in CIF | 3e4w_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/3e4w ftp://data.pdbj.org/pub/pdb/validation_reports/e4/3e4w | HTTPS FTP |
-Related 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34320.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria) Gene: MAP_2744c / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73WB6 |
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-Non-polymers , 5 types, 381 molecules
#2: Chemical | #3: Chemical | ChemComp-HEZ / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-GOL / | #6: 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: 3.33 Å3/Da / Density % sol: 63.09 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 1.5 M 1,6-hexanediol, 0.1 M Na citrate, 13-15 % PEG 20000, 2.5-6.5 % glycerol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 31, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38079 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36.5 Å / Num. all: 75154 / Num. obs: 75154 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.057 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 7350 / Rsym value: 0.48 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model of lower resolution structure based on Fe MAD data Resolution: 1.8→36.5 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→36.5 Å
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Refine LS restraints |
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