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Yorodumi- PDB-1ggj: CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, ASN201A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ggj | ||||||
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Title | CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, ASN201ALA 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.92 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: J.Biol.Chem. / Year: 1996 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: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ggj.cif.gz | 621.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ggj.ent.gz | 505.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ggj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ggj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1ggj_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1ggj_validation.xml.gz | 129.5 KB | Display | |
Data in CIF | 1ggj_validation.cif.gz | 192.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1ggj ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1ggj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 84228.422 Da / Num. of mol.: 4 / Mutation: N201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PN201A / Production host: Escherichia coli (E. coli) / References: UniProt: P21179, catalase #2: Chemical | ChemComp-HDD / #3: 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: 2.08 Å3/Da / Density % sol: 40.99 % | ||||||||||||||||||||||||||||||
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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
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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: 1.92→19.26 Å / Num. all: 211232 / Num. obs: 193708 / % possible obs: 91.7 % / Biso Wilson estimate: 16.5 Å2 |
Reflection shell | Resolution: 1.92→1.97 Å / Num. unique all: 15468 / % possible all: 89.46 |
Reflection | *PLUS Rmerge(I) obs: 0.139 |
Reflection shell | *PLUS % possible obs: 89.5 % / Num. unique obs: 15468 / Rmerge(I) obs: 0.49 |
-Processing
Software |
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Refinement | Resolution: 1.92→87.71 Å Stereochemistry target values: CCP4, REFMAC dictionary, rub.lib Details: REFMAC, WEIGHT MATRIX 0.2. X-plor was also used for refinement.
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Refinement step | Cycle: LAST / Resolution: 1.92→87.71 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 19 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.92 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.288 / Rfactor obs: 0.249 |