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- PDB-1cf9: Structure of the mutant VAL169CYS of catalase HPII from Escherich... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cf9 | ||||||
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Title | Structure of the mutant VAL169CYS of catalase HPII from Escherichia coli | ||||||
![]() | PROTEIN (CATALASE HPII) | ||||||
![]() | OXIDOREDUCTASE / HYDROGEN PEROXIDE / COVALENT MODIFICATIONS | ||||||
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 | ![]() ![]() | ||||||
![]() | Mate, M.J. / Loewen, P.C. / Fita, I. | ||||||
![]() | ![]() Title: Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli. Authors: Mate, M.J. / Sevinc, M.S. / Hu, B. / Bujons, J. / Bravo, J. / Switala, J. / Ens, W. / Loewen, P.C. / Fita, I. #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: 2.8 A Crystal Structure of Catalase Hpii from Escherichia Coli Authors: Bravo, J. / Tormo, J. / Verdaguer, N. / Fita, I. / Betzel, C. / Switala, J. / Loewen, P.C. #3: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Catalase Hpii from Escherichia Coli Authors: Tormo, J. / Fita, I. / Switala, J. / Loewen, P.C. #4: ![]() Title: The Refined Structure of Beef Liver Catalase at 2.5 A Resolution Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 628.6 KB | Display | ![]() |
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PDB format | ![]() | 510.3 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 | ![]() | 132.8 KB | Display | |
Data in CIF | ![]() | 196.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qf7C ![]() 1iphS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 84275.461 Da / Num. of mol.: 4 / Mutation: V169C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | Sequence details | 1IPH A SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH B SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH C SWS ...1IPH A SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH B SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH C SWS P21179 1 - 26 NOT IN ATOMS LIST 1IPH D SWS P21179 1 - 26 NOT IN ATOMS LIST | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion, hanging drop / Details: Bravo, J., (1995) Structure, 3, 491. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9058 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→20 Å / Num. obs: 250445 / % possible obs: 88.3 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 9 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.77→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 86.7 |
Reflection shell | *PLUS % possible obs: 86.7 % |
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Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1IPH Resolution: 1.8→20 Å / SU B: 3.62 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.17
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Displacement parameters | Biso mean: 13.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal target: 0.02 |