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Yorodumi- PDB-2qrw: Crystal structure of Mycobacterium tuberculosis trHbO WG8F mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qrw | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis trHbO WG8F mutant | ||||||
Components | Hemoglobin-like protein HbO | ||||||
Keywords | TRANSPORT PROTEIN / truncated hemoglobin fold / alpha helix / Heme / Hydroxylation / Iron / Membrane / Metal-binding / Oxygen transport / Transport | ||||||
Function / homology | Function and homology information oxygen transport / oxygen carrier activity / oxygen binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Milani, M. / Bolognesi, M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: The Roles of Tyr(CD1) and Trp(G8) in Mycobacterium tuberculosis Truncated Hemoglobin O in Ligand Binding and on the Heme Distal Site Architecture Authors: Ouellet, H. / Milani, M. / LaBarre, M. / Bolognesi, M. / Couture, M. / Guertin, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qrw.cif.gz | 374.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qrw.ent.gz | 308.2 KB | Display | PDB format |
PDBx/mmJSON format | 2qrw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/2qrw ftp://data.pdbj.org/pub/pdb/validation_reports/qr/2qrw | HTTPS FTP |
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-Related structure data
Related structure data | 1ngkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 14932.825 Da / Num. of mol.: 12 / Mutation: W88F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glbO / Production host: Escherichia coli (E. coli) / References: UniProt: P0A595, UniProt: P9WN23*PLUS #2: Chemical | ChemComp-CYN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-HEM / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 2.2 M ammonium sulfate, 0.05 M phosphate buffer, 0.001 M KCN, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Detector: CCD / Date: Oct 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→47.67 Å / Num. obs: 178559 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.3 / Num. unique all: 23850 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ngk Resolution: 1.93→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.513 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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