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- PDB-1gge: CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, NATIVE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gge | ||||||
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Title | CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, NATIVE STRUCTURE AT 1.9 A RESOLUTION. | ||||||
![]() | PROTEIN (CATALASE HPII) | ||||||
![]() | OXIDOREDUCTASE / BETA BARREL / ALPHA HELICAL DOMAIN / FLAVODOXIN LIKE DOMAIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
Model details | THE STRUCTURE CONTAINS OXIDIZED FORM OF PROTOPORFIRIN IX, WHICH IS CALLED HEM-D, AND COVALENT BOND ...THE STRUCTURE CONTAINS OXIDIZED FORM OF PROTOPORFIRIN IX, WHICH IS CALLED HEM-D, AND COVALENT BOND BETWEEN HIS392-TYR415. | ||||||
![]() | Melik-Adamyan, W.R. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Structure of the Heme D of Penicillium Vitale and Escherichia Coli Catalases Authors: Murshudov, G.N. / Grebenko, A.I. / Barynin, V. / Dauter, Z. / Wilson, K.S. / Vainshtein, B.K. / Melik-Adamyan, W.R. / Bravo, J. / Ferran, J.M. / Ferrer, J.C. / Switala, J. / Loewen, P.C. / Fita, I. #3: ![]() 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.S. / Loewen, P.C. / Fita, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 634.5 KB | Display | ![]() |
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PDB format | ![]() | 516.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 133.4 KB | Display | |
Data in CIF | ![]() | 200.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 84271.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HDD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 3350, LiCl, Tris-HCl, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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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 | Relative weight: 1 |
Reflection | Resolution: 1.89→17.96 Å / Num. obs: 214389 / % possible obs: 97.7 % / Biso Wilson estimate: 19.1 Å2 |
Reflection shell | Resolution: 1.89→1.94 Å / % possible all: 88.4 |
Reflection | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 17.96 Å / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 88.4 % / Num. unique obs: 16094 / Rmerge(I) obs: 0.269 |
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Processing
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Refinement | Resolution: 1.89→87.6 Å Details: REFMAC, WEIGHT MATRIX 0.2. X-Plor was also used for refinement.
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Refinement step | Cycle: LAST / Resolution: 1.89→87.6 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 18 Å / Rfactor obs: 0.166 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 1.94 Å / Rfactor Rfree: 0.232 / Rfactor obs: 0.189 |