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Yorodumi- PDB-1s56: Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s56 | ||||||
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Title | Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Xe Atoms | ||||||
Components | Hemoglobin-like protein HbN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / GROUP I TRUNCATED HEMOGLOBIN / 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 / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Milani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Heme-ligand tunneling in group I truncated hemoglobins Authors: Milani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s56.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s56.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 1s56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/1s56 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/1s56 | HTTPS FTP |
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-Related structure data
Related structure data | 1s61C 1uvxC 1uvyC 1rteS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14464.515 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: GLBN, RV1542C, MT1594, MTCY48.23, MB1569C / Production host: Escherichia coli (E. coli) / References: UniProt: P0A592, UniProt: P9WN25*PLUS |
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-Non-polymers , 7 types, 121 molecules
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-HEC / | #5: Chemical | ChemComp-XE / #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-HEM / | #8: 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: 2.15 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: phosphate, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 22, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→50 Å / Num. all: 9301 / Num. obs: 9301 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.098 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.43→2.56 Å / Redundancy: 4 % / Rsym value: 0.277 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1RTE Resolution: 2.43→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.732 / ESU R Free: 0.346 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.003 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.433→2.496 Å / Total num. of bins used: 20 /
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