[English] 日本語
Yorodumi- PDB-6ztx: Crystal Structure of catalase HPII from Escherichia coli (serendi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ztx | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized) | ||||||||||||
Components | Catalase HPII | ||||||||||||
Keywords | OXIDOREDUCTASE / catalase / hydrogen-peroxide / heme / iron / oxidative stress / artifact crystallization / impurities / contaminations | ||||||||||||
Function / homology | Function and homology information catalase / hyperosmotic response / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / DNA damage response / heme binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||||||||
Authors | Grzechowiak, M. / Sekula, B. / Ruszkowski, M. | ||||||||||||
Funding support | Poland, United States, 3items
| ||||||||||||
Citation | Journal: Acta Biochim.Pol. / Year: 2021 Title: Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told". Authors: Grzechowiak, M. / Sekula, B. / Jaskolski, M. / Ruszkowski, M. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ztx.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ztx.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6ztx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ztx_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ztx_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6ztx_validation.xml.gz | 128.5 KB | Display | |
Data in CIF | 6ztx_validation.cif.gz | 196.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/6ztx ftp://data.pdbj.org/pub/pdb/validation_reports/zt/6ztx | HTTPS FTP |
-Related structure data
Related structure data | 6ztvC 6ztwC 1ggeS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 84144.148 Da / Num. of mol.: 4 / Mutation: R37S, S99D, K372N, R521S / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: UniProt: P21179, catalase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-HDD / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 670790 / % possible obs: 98.3 % / Redundancy: 4.84 % / Biso Wilson estimate: 11.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.115 / Net I/σ(I): 11.78 |
Reflection shell | Resolution: 1.3→1.38 Å / Redundancy: 4.86 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 2 / Num. unique obs: 106698 / CC1/2: 0.59 / Rrim(I) all: 1.236 / % possible all: 96.9 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gge Resolution: 1.3→44.76 Å / SU ML: 0.1299 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 15.797 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.76 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→44.76 Å
| ||||||||||||||||||||||||
Refine LS restraints |
|