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Yorodumi- PDB-5nri: Crystal structure of Burkholderia pseudomallei D-alanine-D-alanin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nri | ||||||
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Title | Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala | ||||||
Components | D-alanine--D-alanine ligase | ||||||
Keywords | LIGASE / complex | ||||||
Function / homology | Function and homology information D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Diaz-Saez, L. / Hunter, W.N. | ||||||
Citation | Journal: Febs J. / Year: 2019 Title: Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target. Authors: Diaz-Saez, L. / Torrie, L.S. / McElroy, S.P. / Gray, D. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nri.cif.gz | 298.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nri.ent.gz | 241.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/5nri ftp://data.pdbj.org/pub/pdb/validation_reports/nr/5nri | HTTPS FTP |
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-Related 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: 33378.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: ddl, BURPS1106A_3548 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3NZL3, D-alanine-D-alanine ligase |
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-Non-polymers , 7 types, 806 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-PGE / | #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: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.05 to 0.3 M Li2SO4, 0.1 M Bis-Tris pH 5.5 and 15-30% (w/v) PEG 3350, ratio protein:reservoir 1:1 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→69.97 Å / Num. obs: 90609 / % possible obs: 96.6 % / Redundancy: 3.1 % / Net I/σ(I): 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: see publication Resolution: 1.5→69.97 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.339 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / 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: 26.004 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→69.97 Å
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