+Open data
-Basic information
Entry | Database: PDB / ID: 1o16 | ||||||
---|---|---|---|---|---|---|---|
Title | RECOMBINANT SPERM WHALE MYOGLOBIN H64D/V68S/D122N MUTANT (MET) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / MYOGLOBIN / ENZYME / SULFOXIDATION / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / ISOMORPHIC WITH WILD-TYPE / Resolution: 1.95 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 | 1o16.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1o16.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1o16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/1o16 ftp://data.pdbj.org/pub/pdb/validation_reports/o1/1o16 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17330.051 Da / Num. of mol.: 1 / Mutation: H64D,V68S,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: 61.27 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 9 / Details: pH 9.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / 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 |
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: 1.95→19 Å / Num. obs: 14391 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.95→2.08 Å / % possible all: 80.9 |
Reflection | *PLUS % possible obs: 89.7 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ISOMORPHIC WITH WILD-TYPE / Resolution: 1.95→18.18 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 143.411 Å2 / ksol: 0.639318 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→18.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.19 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|