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Yorodumi- PDB-7l3y: Crystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H spe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l3y | ||||||
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Title | Crystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H sperm whale myoglobin; partial occupancy) | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / globin / oxidase / oxygen binding / oxygen reduction / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Petrik, I. / Lu, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2021 Title: An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Authors: Petrik, I.D. / Davydov, R. / Kahle, M. / Sandoval, B. / Dwaraknath, S. / Adelroth, P. / Hoffman, B. / Lu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l3y.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l3y.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 7l3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/7l3y ftp://data.pdbj.org/pub/pdb/validation_reports/l3/7l3y | HTTPS FTP |
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-Related structure data
Related structure data | 7kyrC 7l3uC 4fwxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17398.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-PER / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000. After ...Details: 1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000. After crystalization, soaked, under anaerobic conditions, in 20 mM dithionite for 10 minutes, and washed with anaerobic buffer. Reduced crystals were sealed in an air-tight bomb and pressurized at ~1500 psi O2 for up to 10 minutes. Crystals were harvested and cryocooled after a brief soak in 50% PEG 400 supersaturated with O2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.18→39.02 Å / Num. obs: 47352 / % possible obs: 97 % / Redundancy: 3.9 % / CC1/2: 1 / Rmerge(I) obs: 0.024 / Rpim(I) all: 0.013 / Rrim(I) all: 0.028 / Net I/σ(I): 31.7 / Num. measured all: 182510 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FWX Resolution: 1.18→39.02 Å / SU ML: 0.1094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.559 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: 17.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→39.02 Å
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Refine LS restraints |
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LS refinement shell |
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