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Yorodumi- PDB-5ab8: High resolution X-ray structure of the N-terminal truncated form ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ab8 | ||||||
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Title | High resolution X-ray structure of the N-terminal truncated form (residues 1-11) of Mycobacterium tuberculosis HbN | ||||||
Components | GROUP 1 TRUNCATED HEMOGLOBIN GLBN | ||||||
Keywords | OXYGEN TRANSPORT / TRUNCATED HEMOGLOBINS / 2/2 HEMOGLOBINS / GLOBIN DYNAMICS / BACTERIAL GLOBINS / HEME/LIGAND TUNNELING / NO DIOXYGENASE | ||||||
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: 1.53 Å | ||||||
Authors | Pesce, A. / Bustamante, J.P. / Bidon-Chanal, A. / Boechi, L. / Estrin, D.A. / Luque, F.J. / Sebilo, A. / Guertin, M. / Bolognesi, M. / Ascenzi, P. / Nardini, M. | ||||||
Citation | Journal: FEBS J. / Year: 2016 Title: The N-Terminal Pre-A Region of Mycobacterium Tuberculosis 2/2Hbn Promotes No-Dioxygenase Activity. Authors: Pesce, A. / Bustamante, J.P. / Bidon-Chanal, A. / Boechi, L. / Estrin, D.A. / Luque, F.J. / Sebilo, A. / Guertin, M. / Bolognesi, M. / Ascenzi, P. / Nardini, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ab8.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ab8.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ab8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5ab8 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5ab8 | HTTPS FTP |
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-Related structure data
Related structure data | 1idrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13119.839 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 12-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P9WN25 |
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-Non-polymers , 5 types, 153 molecules
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-FMT / | ||
#4: Chemical | ChemComp-ACT / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | HEME (HEM): THE HEME VYNIL GROUP IS COVALENTLY MODIFIED AT THE CBB ATOM. THE MODIFICATION HAS NOT ...HEME (HEM): THE HEME VYNIL GROUP IS COVALENTLY |
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Sequence details | OUR PROTEIN CONSTRUCT START FROM RESIDUE 12. RESIDUES FROM 129 TO 136 WERE NOT LOCATED IN THE ...OUR PROTEIN CONSTRUCT START FROM RESIDUE 12. RESIDUES FROM 129 TO 136 WERE NOT LOCATED IN THE EXPERIMENT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.62 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 4.6 / Details: 2.0 M NA-FORMATE, 0.1 M NA-ACETATE PH 4.6, T=277 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→53.23 Å / Num. obs: 18944 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 15.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 15.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IDR Resolution: 1.53→33.07 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.09 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 129-136 WERE NOT LOCATED IN THE EXPERIMENT THE HEME VINYL GROUP WAS COVALENTLY MODIFIED AT THE CBB ATOM. THE MODIFICATION HAS NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 129-136 WERE NOT LOCATED IN THE EXPERIMENT THE HEME VINYL GROUP WAS COVALENTLY MODIFIED AT THE CBB ATOM. THE MODIFICATION HAS NOT BEEN MODELED IN THE STRUCTURE
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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: 27.522 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→33.07 Å
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Refine LS restraints |
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