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Yorodumi- PDB-3e5n: Crystal structure of D-alanine-D-alanine ligase from Xanthomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e5n | ||||||
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Title | Crystal structure of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331 | ||||||
Components | D-alanine-D-alanine ligase A | ||||||
Keywords | LIGASE / Bacterial blight / D-alanine-D-alanine ligase / PIP (Plant-Inducible Promoter) box peptidoglycan biosynthesis Xanthomonas oryzae pv. oryzae / ATP-binding / Cell shape / Cell wall biogenesis/degradation / Cytoplasm / Magnesium / Manganese / Metal-binding / Nucleotide-binding / Peptidoglycan synthesis | ||||||
Function / homology | Function and homology information Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Xanthomonas oryzae pv. oryzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Doan, T.N.T. / Kim, J.K. / Kim, H.S. / Ahn, Y.J. / Kim, J.G. / Lee, B.M. / Kang, L.W. | ||||||
Citation | Journal: To be published Title: Crystal structure of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331 Authors: Doan, T.N.T. / Kim, J.K. / Kim, H.S. / Ahn, Y.J. / Kim, J.G. / Lee, B.M. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e5n.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e5n.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 3e5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e5n_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 3e5n_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3e5n_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 3e5n_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/3e5n ftp://data.pdbj.org/pub/pdb/validation_reports/e5/3e5n | HTTPS FTP |
-Related structure data
Related structure data | 2nmpS 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
#1: Protein | Mass: 41945.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria) Strain: MAFF 311018 / Gene: XOO0324 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q2P8P8 |
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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: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15%(w/v) PEG4000, 0.1M Tris, pH8.5, 0.2M MgCl2, 0.3M Dimethylethyl-(3-Sulfopropyl)-ammonium, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2008 |
Radiation | Monochromator: flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 23816 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NMP Resolution: 2→38.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.343 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / 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: 36.893 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.05 Å / Total num. of bins used: 20
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