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- PDB-1jkv: Crystal Structure of Manganese Catalase from Lactobacillus planta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jkv | ||||||
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Title | Crystal Structure of Manganese Catalase from Lactobacillus plantarum complexed with azide | ||||||
![]() | pseudocatalase | ||||||
![]() | OXIDOREDUCTASE / hexamer / catalase dimanganese / metalloenzyme | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barynin, V.V. / Whittaker, M.M. / Antonyuk, S.V. / Lamzin, V.S. / Harrison, P.M. / Artymiuk, P.J. / Whittaker, J.W. | ||||||
![]() | ![]() Title: Crystal structure of manganese catalase from Lactobacillus plantarum. Authors: Barynin, V.V. / Whittaker, M.M. / Antonyuk, S.V. / Lamzin, V.S. / Harrison, P.M. / Artymiuk, P.J. / Whittaker, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 682.7 KB | Display | ![]() |
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PDB format | ![]() | 558.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.9 KB | Display | ![]() |
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Full document | ![]() | 428.1 KB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 56.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jkuSC 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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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 29779.379 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 6 types, 1591 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/MN3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/MN3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-OH / #4: Chemical | ChemComp-AZI / #5: Chemical | ChemComp-MN3 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.15 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: PEG 8000, TAPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K, pH 8.7 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→17 Å / Num. all: 269006 / Num. obs: 269006 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Rsym value: 5 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.39→1.43 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.1 / Num. unique all: 15234 / Rsym value: 14 / % possible all: 78.3 |
Reflection | *PLUS Highest resolution: 1.4 Å / Num. measured all: 663270 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å / % possible obs: 78.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.13 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JKU Resolution: 1.39→17 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.975 Å2
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Refinement step | Cycle: LAST / Resolution: 1.39→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.39→1.43 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 17 Å / Num. reflection Rfree: 13288 / % reflection Rfree: 5 % / Rfactor all: 0.1037 / Rfactor obs: 0.10509 / Rfactor Rfree: 0.13 / Rfactor Rwork: 0.104 | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.172 / Rfactor Rwork: 0.119 |