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- PDB-6ro8: The crystal structure of Acinetobacter radioresistens CYP116B5 he... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ro8 | ||||||
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Title | The crystal structure of Acinetobacter radioresistens CYP116B5 heme domain | ||||||
![]() | Cytochrome P450 RhF | ||||||
![]() | OXIDOREDUCTASE / cytochrome P450 / monooxygenases / biocatalysis | ||||||
Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ciaramella, A. / Catucci, G. / Gilardi, G. / Di Nardo, G. | ||||||
![]() | ![]() Title: Crystal structure of bacterial CYP116B5 heme domain: New insights on class VII P450s structural flexibility and peroxygenase activity. Authors: Ciaramella, A. / Catucci, G. / Gilardi, G. / Di Nardo, 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 | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 599 KB | Display | ![]() |
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Full document | ![]() | 606.1 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6giiS S: Starting model for refinement |
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Similar 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: 51896.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-HIS / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.19 Å3/Da / Density % sol: 76.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM amino acids (0.02 M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L- ...Details: 100 mM amino acids (0.02 M DL-Arginine hydrochloride, 0.02M DL-Threonine, 0.02M DL-Histidine monohydrochloride monohydrate, 0.02M DL-5-Hydroxylysine hydrochloride, 0.02M trans-4-hydroxy-L-proline), 0.1 M Gly-Gly, AMPD buffer pH 8.5, 50% v/v of 25% w/v PEG 4000, 40% w/v 1,2,6- Hexanetriol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→109.9 Å / Num. obs: 31654 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 73.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Net I/av σ(I): 19.9 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3788 / CC1/2: 0.584 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GII Resolution: 2.6→91.33 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 202.59 Å2 / Biso mean: 88.6208 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→91.33 Å
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