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Yorodumi- PDB-1nwa: Structure of Mycobacterium tuberculosis Methionine Sulfoxide Redu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nwa | ||||||
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Title | Structure of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A in Complex with Protein-bound Methionine | ||||||
Components | Peptide methionine sulfoxide reductase msrA | ||||||
Keywords | OXIDOREDUCTASE / peptide methionine sulfoxide reductase / product complex / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information L-methionine-(S)-S-oxide reductase activity / L-methionine:thioredoxin-disulfide S-oxidoreductase activity / Tolerance by Mtb to nitric oxide produced by macrophages / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / response to nitrosative stress / protein modification process => GO:0036211 / cellular response to oxidative stress / response to oxidative stress / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Taylor, A.B. / Benglis Jr., D.M. / Dhandayuthapani, S. / Hart, P.J. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: Structure of Mycobacterium tuberculosis Methionine Sulfoxide Reductase A in Complex with Protein-bound Methionine Authors: Taylor, A.B. / Benglis Jr., D.M. / Dhandayuthapani, S. / Hart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nwa.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nwa.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nwa_validation.pdf.gz | 419.8 KB | Display | wwPDB validaton report |
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Full document | 1nwa_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | 1nwa_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1nwa_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nwa ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nwa | HTTPS FTP |
-Related structure data
Related structure data | 1ff3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23041.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MSRA / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P0A5L0, UniProt: P9WJM5*PLUS, EC: 1.8.4.6 |
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#2: 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: 2.12 Å3/Da / Density % sol: 41.52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium formate, sodium citrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 7, 2002 / Details: mirrors |
Radiation | Monochromator: confocal multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 30701 / Num. obs: 30701 / % possible obs: 97.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2915 / % possible all: 94.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 30657 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 94.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FF3 Resolution: 1.5→48.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.064 / 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: 13.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→48.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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