+Open data
-Basic information
Entry | Database: PDB / ID: 5yzf | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of met K42C sperm whale myoglobin | ||||||
Components | sperm whale myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / myoglobin | ||||||
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: 1.77 Å | ||||||
Authors | Yuan, H. | ||||||
Citation | Journal: J. Inorg. Biochem. / Year: 2018 Title: Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen Authors: Cheng, H.M. / Yuan, H. / Wang, X.J. / Xu, J.K. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yzf.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yzf.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 5yzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/5yzf ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yzf | HTTPS FTP |
---|
-Related structure data
Related structure data | 101mS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17340.111 Da / Num. of mol.: 1 / Mutation: K43C 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-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 15228 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Rsym value: 0.117 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.503 / Rpim(I) all: 0.228 / Rsym value: 0.501 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 101M Resolution: 1.77→34.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.27 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.425 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.77→34.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|