[English] 日本語
Yorodumi- PDB-2gkn: Crystal structure of Mycobacterium tuberculosis trHbN, GlnE11Val ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gkn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis trHbN, GlnE11Val mutant | ||||||
Components | Hemoglobin-like protein HbN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / truncated hemoglobin / mutant / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information detoxification of nitrogen compound / Tolerance by Mtb to nitric oxide produced by macrophages / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / thioredoxin peroxidase activity / cell redox homeostasis / oxygen carrier activity / oxygen binding / cellular response to oxidative stress / heme binding ...detoxification of nitrogen compound / Tolerance by Mtb to nitric oxide produced by macrophages / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / thioredoxin peroxidase activity / cell redox homeostasis / oxygen carrier activity / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Milani, M. / Bolognesi, M. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Ligand interactions in the distal heme pocket of Mycobacterium tuberculosis truncated hemoglobin N: roles of TyrB10 and GlnE11 residues Authors: Ouellet, Y. / Milani, M. / Couture, M. / Bolognesi, M. / Guertin, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gkn.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gkn.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/2gkn ftp://data.pdbj.org/pub/pdb/validation_reports/gk/2gkn | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14435.517 Da / Num. of mol.: 2 / Mutation: YB10F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glbN / Production host: Escherichia coli (E. coli) / References: UniProt: P0A592, UniProt: P9WN25*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.6 Details: di-potassium hydrogen phosphate + sodium dihydrogen phosphate 1.8 M, pH 7.6, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Detector: CCD / Date: Jul 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→51.43 Å / Num. all: 10631 / Num. obs: 10631 / % possible obs: 73.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.143 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 1.4 / % possible all: 64.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→51.43 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.864 / SU B: 6.929 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.451 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.359 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→51.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
|