[English] 日本語
Yorodumi- PDB-1ggk: CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, ASN201H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ggk | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, ASN201HIS VARIANT. | ||||||
Components | CATALASE HPII | ||||||
Keywords | OXIDOREDUCTASE / BETA BARREL / ALPHA HELICAL DOMAIN / FLAVODOXIN LIKE DOMAIN | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.26 Å | ||||||
Authors | Melik-Adamyan, W.R. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli. Authors: Melik-Adamyan, W. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C. #1: Journal: Structure / Year: 1995 Title: Crystal Structure of Catalase HPII from Escherichia coli Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I. #2: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 1999 Title: Structure of Catalase HpII from Escherichia Coli at 1.9 A Resolution Authors: Bravo, J. / Mate, M.J. / Schneider, T. / Switala, J. / Wilson, K. / Loewen, P.C. / Fita, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ggk.cif.gz | 602.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ggk.ent.gz | 491.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ggk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1ggk ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1ggk | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 84295.500 Da / Num. of mol.: 4 / Mutation: N201H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PN201H / Production host: Escherichia coli (E. coli) / References: UniProt: P21179, catalase #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.87 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 3350, LiCl, Tris-HCl, pH 9.0, vapor diffusion/hanging drop, temperature 297.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→12.54 Å / Num. all: 137735 / Num. obs: 120733 / % possible obs: 88.2 % / Biso Wilson estimate: 26 Å2 |
Reflection shell | Resolution: 2.26→2.32 Å / Num. unique all: 10095 / % possible all: 68.4 |
Reflection | *PLUS Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 68.4 % / Num. unique obs: 10095 / Rmerge(I) obs: 0.355 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.26→117.38 Å / Stereochemistry target values: CCP4, protin_jp.idl Details: REFMAC, WEIGHT MATRIX 0.2. X-Plor was also used during refinement.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→117.38 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.13 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.271 / Rfactor obs: 0.183 |