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Yorodumi- PDB-5jzx: Crystal Structure of UDP-N-acetylenolpyruvoylglucosamine reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jzx | ||||||
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Title | Crystal Structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Mycobacterium tuberculosis | ||||||
Components | UDP-N-acetylenolpyruvoylglucosamine reductase | ||||||
Keywords | OXIDOREDUCTASE / Reductase / Peptidoglycan synthesis / NADPH Oxidation / Rossmann Fold | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dharavath, S. / Eniyan, K. / Bajpai, U. / Gourinath, S. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: Crystal structure of UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Mycobacterium tuberculosis Authors: Eniyan, K. / Dharavath, S. / Vijayan, R. / Bajpai, U. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jzx.cif.gz | 395.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jzx.ent.gz | 318 KB | Display | PDB format |
PDBx/mmJSON format | 5jzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jzx_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5jzx_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5jzx_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 5jzx_validation.cif.gz | 104.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/5jzx ftp://data.pdbj.org/pub/pdb/validation_reports/jz/5jzx | HTTPS FTP |
-Related structure data
Related structure data | 1uxyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42395.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: murB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) References: UniProt: P9WJL9, UDP-N-acetylmuramate dehydrogenase #2: Chemical | ChemComp-FAD / #3: Chemical | #4: 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: 3.02 Å3/Da / Density % sol: 59.26 % / Description: cube shaped crystal |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.8M sodium formate, 15% PEG 4000, 0.2M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 3, 2015 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 192931 / % possible obs: 98.8 % / Redundancy: 4 % / Net I/σ(I): 2.13 |
Reflection shell | Resolution: 2.17→2.22 Å |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UXY Resolution: 2.2→38.427 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.405 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.199 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.347 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→38.427 Å
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