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Yorodumi- PDB-6r3w: M.tuberculosis nitrobindin with a water molecule coordinated to t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r3w | ||||||
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Title | M.tuberculosis nitrobindin with a water molecule coordinated to the heme iron atom | ||||||
Components | UPF0678 fatty acid-binding protein-like protein ERS007657_00996 | ||||||
Keywords | PROTEIN BINDING / heme-protein / beta-barrel / peroxynitrite detossification | ||||||
Function / homology | Function and homology information peroxynitrite isomerase activity / Isomerases; Other isomerases / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | De Simone, G. / di Masi, A. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. ...De Simone, G. / di Masi, A. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. / Abbruzzetti, S. / Viappiani, C. / Bruno, S. / Ascenzi, P. | ||||||
Citation | Journal: Antioxid.Redox Signal. / Year: 2020 Title: Mycobacterial and Human Nitrobindins: Structure and Function. Authors: De Simone, G. / di Masi, A. / Vita, G.M. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. ...Authors: De Simone, G. / di Masi, A. / Vita, G.M. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. / Abbruzzetti, S. / Viappiani, C. / Bruno, S. / Ascenzi, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r3w.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r3w.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r3w_validation.pdf.gz | 787.5 KB | Display | wwPDB validaton report |
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Full document | 6r3w_full_validation.pdf.gz | 788 KB | Display | |
Data in XML | 6r3w_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 6r3w_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r3w ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r3w | HTTPS FTP |
-Related structure data
Related structure data | 6r3yC 2fr2S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18940.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: ERS007657_00996, ERS007661_00585, ERS007665_01763, ERS007670_02052, ERS007672_00691, ERS007679_01339, ERS007681_01416, ERS007688_01403, ERS007703_01571, ERS007720_01340, ERS007722_02241, ...Gene: ERS007657_00996, ERS007661_00585, ERS007665_01763, ERS007670_02052, ERS007672_00691, ERS007679_01339, ERS007681_01416, ERS007688_01403, ERS007703_01571, ERS007720_01340, ERS007722_02241, ERS007726_02281, ERS007734_00360, ERS007737_00208, ERS007741_02326, ERS023446_01189, ERS024213_01977, ERS027644_00434, ERS027646_00714, ERS027651_02146, ERS027652_02045, ERS027653_02567, ERS027656_02331, ERS027659_01673, ERS027661_03351, ERS027666_00865, ERS031537_00196, ERS124361_02201, SAMEA2682864_02059, SAMEA2683035_01682 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) Strain (production host): BL21 / References: UniProt: A0A0E8TXJ8, UniProt: P9WFG7*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.63 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris, PEG 4k 30% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→48.5 Å / Num. obs: 54078 / % possible obs: 95 % / Redundancy: 12.4 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6047 / % possible all: 74.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2fr2 Resolution: 1.2→47.09 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.353 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.038 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.814 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→47.09 Å
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Refine LS restraints |
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