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- PDB-6ds8: Crystal structure of MhuD R26S mutant with two Manganese protopor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ds8 | |||||||||
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Title | Crystal structure of MhuD R26S mutant with two Manganese protoporphyrin IX bound per active site | |||||||||
![]() | Heme-degrading monooxygenase HmoB | |||||||||
![]() | OXIDOREDUCTASE / Heme Oxygenase (decyclizing) Activity / Monooxygenase Activity / Oxidoreductase Activity / Heme Binding / Metal Ion Binding / Heme Catabolic Process / Oxidation Reduction Process / Cell Wall / Plasma Membrane | |||||||||
Function / homology | ![]() heme oxygenase (mycobilin-producing) / heme oxygenase (decyclizing) activity / heme catabolic process / peptidoglycan-based cell wall / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chao, A. / Goulding, C.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of MhuD R26S mutant with two Manganese protoporphyrin IX bound per active site Authors: Chao, A. / Goulding, C.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 | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hx9S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 100 / Label seq-ID: 1 - 99
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Components
#1: Protein | Mass: 10537.784 Da / Num. of mol.: 2 / Mutation: R26S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: mhuD, Rv3592 / Production host: ![]() ![]() References: UniProt: P9WKH3, heme oxygenase (biliverdin-producing) #2: Chemical | ChemComp-MNH / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.502 Å / Num. obs: 7868 / % possible obs: 95.06 % / Redundancy: 2 % / Biso Wilson estimate: 30.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01736 / Rpim(I) all: 0.01736 / Rrim(I) all: 0.02455 / Net I/σ(I): 26.25 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 0.08277 / Mean I/σ(I) obs: 7.58 / Num. unique obs: 760 / CC1/2: 0.98 / Rpim(I) all: 0.08277 / Rrim(I) all: 0.1171 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HX9 Resolution: 2.4→50.502 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.26 Å2 / Biso mean: 30.6722 Å2 / Biso min: 10.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→50.502 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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