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Yorodumi- PDB-1idr: CRYSTAL STRUCTURE OF THE TRUNCATED-HEMOGLOBIN-N FROM MYCOBACTERIU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1idr | ||||||
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Title | CRYSTAL STRUCTURE OF THE TRUNCATED-HEMOGLOBIN-N FROM MYCOBACTERIUM TUBERCULOSIS | ||||||
Components | HEMOGLOBIN HBN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / truncated hemoglobin fold / 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: 1.9 Å | ||||||
Authors | Milani, M. / Pesce, A. / Ascenzi, P. / Guertin, M. / Bolognesi, M. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme. Authors: Milani, M. / Pesce, A. / Ouellet, Y. / Ascenzi, P. / Guertin, M. / Bolognesi, M. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Gel-filtration experiment indicates that the protein is loosely dimeric. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1idr.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1idr.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1idr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idr ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14464.515 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A592, UniProt: P9WN25*PLUS #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.19 Å3/Da / Density % sol: 43.9 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 8.3 Details: potassium phosphate, pH 8.3, MICRODIALYSIS, temperature 277K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||
Components of the solutions | *PLUS
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-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 | Type: MARRESEARCH / Detector: CCD / Date: Apr 27, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 190583 / Num. obs: 18688 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.331 / % possible all: 88.9 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 95.1 % / Redundancy: 3.5 % / Num. measured all: 190583 |
Reflection shell | *PLUS % possible obs: 88.9 % / Redundancy: 2.3 % / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / SU B: 4.43152 / SU ML: 0.12857 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17577 / ESU R Free: 0.16852 / Stereochemistry target values: Engh and Huber
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Displacement parameters | Biso mean: 32.725 Å2
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Refine analyze | Luzzati sigma a obs: 0.04 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5.2 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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