+Open data
-Basic information
Entry | Database: PDB / ID: 2g11 | ||||||
---|---|---|---|---|---|---|---|
Title | Photolyzed CO L29F Myoglobin: 31.6ns | ||||||
Components | Myoglobin | ||||||
Keywords | TRANSPORT PROTEIN / Time-resolved crystallography / myoglobin / difference refinement / structure-function relationship / intermediate states | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Aranda, R. / Levin, E.J. / Schotte, F. / Anfinrud, P.A. / Phillips Jr., G.N. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin. Authors: Aranda, R. / Levin, E.J. / Schotte, F. / Anfinrud, P.A. / Phillips Jr., G.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2g11.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2g11.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 2g11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g11_validation.pdf.gz | 799.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2g11_full_validation.pdf.gz | 802.3 KB | Display | |
Data in XML | 2g11_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 2g11_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/2g11 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/2g11 | HTTPS FTP |
-Related structure data
Related structure data | 2g0rC 2g0sC 2g0vC 2g0xC 2g0zC 2g10C 2g12C 2g14C 2splS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Number of models | 2 |
-Components
#1: Protein | Mass: 17399.180 Da / Num. of mol.: 1 / Mutation: L29F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CMO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.99 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 9 Details: 2.6M Ammonium Sulfate, 20mM TrisHCl, 1mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 9.00 |
-Data collection
Diffraction | Mean temperature: 283 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.79 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 1, 2002 |
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.79 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.881 Å / Num. obs: 21924 / Biso Wilson estimate: 19 Å2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 2SPL Resolution: 1.9→29.88 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1650815.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DIFFERENCE REFINEMENT (TERWILLIGER 1995
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|