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- PDB-6z4r: sperm whale myoglobin mutant (H64V V64A) bearing the non-canonica... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z4r | |||||||||
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Title | sperm whale myoglobin mutant (H64V V64A) bearing the non-canonical amino acid 3-thienylalanine as axial heme ligand | |||||||||
![]() | Myoglobin | |||||||||
![]() | METAL BINDING PROTEIN / Globin / Heme protein / Enzyme | |||||||||
Function / homology | ![]() nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tinzl, M. / Hilvert, D. / Mittl, P.R.E. | |||||||||
![]() | ![]() Title: Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*. Authors: Pott, M. / Tinzl, M. / Hayashi, T. / Ota, Y. / Dunkelmann, D. / Mittl, P.R.E. / Hilvert, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.4 KB | Display | ![]() |
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Full document | ![]() | 796.6 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z4tC ![]() 6g5tS 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
#1: Protein | Mass: 17254.016 Da / Num. of mol.: 1 / Mutation: H64V V68A H93(3ThiA) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M SPG buffer 28-32% PEG 1500 180 nL protein 10 mg/mL + 20 nL seed 100 nL well solution PH range: 6.8-7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000031 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 20069 / % possible obs: 99.3 % / Redundancy: 6.77 % / CC1/2: 0.996 / Net I/σ(I): 8.16 |
Reflection shell | Resolution: 1.96→2.08 Å / Num. unique obs: 3194 / CC1/2: 0.731 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6G5T Resolution: 1.96→40.16 Å / SU ML: 0.2898 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5172 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→40.16 Å
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Refine LS restraints |
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LS refinement shell |
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