+Open data
-Basic information
Entry | Database: PDB / ID: 1lue | ||||||
---|---|---|---|---|---|---|---|
Title | RECOMBINANT SPERM WHALE MYOGLOBIN H64D/V68A/D122N MUTANT (MET) | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / myoglobin / enzyme / sulfoxidation / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information 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 | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Isomorphic with wild-type / Resolution: 1.7 Å | ||||||
Authors | Phillips Jr., G.N. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Molecular engineering of myoglobin: influence of residue 68 on the rate and the enantioselectivity of oxidation reactions catalyzed by H64D/V68X myoglobin Authors: Yang, H.J. / Matsui, T. / Ozaki, S. / Kato, S. / Ueno, T. / Phillips Jr., G.N. / Fukuzumi, S. / Watanabe, Y. #1: Journal: J.AM.CHEM.SOC. / Year: 2002 Title: ASYMMETRIC SULFOXIDATION AND AMINE BINDING BY H64D/V68A AND H64D/V68S MB: MECHANISTIC INSIGHT INTO THE CHIRAL DISCRIMINATION STEP Authors: Kato, S. / Yang, H.J. / Ueno, T. / Ozaki, S. / Phillips Jr., G.N. / Fukuzumi, S. / Watanabe, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lue.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lue.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lue_validation.pdf.gz | 799.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lue_full_validation.pdf.gz | 800.7 KB | Display | |
Data in XML | 1lue_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1lue_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1lue ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1lue | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17314.051 Da / Num. of mol.: 1 / Mutation: H64D,V68A,D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.3 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: ammonium sulfate, tris-HCL, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 7, 2000 |
Radiation | Monochromator: LONG SUPPER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19 Å / Num. all: 22467 / Num. obs: 22467 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.7→1.81 Å / % possible all: 73.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Isomorphic with wild-type / Resolution: 1.7→18.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1705475.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.5393 Å2 / ksol: 0.37493 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→18.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|