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Yorodumi- PDB-6ue0: Crystal structure of dihydrodipicolinate synthase from Klebsiella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ue0 | ||||||||||||
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Title | Crystal structure of dihydrodipicolinate synthase from Klebsiella pneumoniae bound to pyruvate | ||||||||||||
Components | 4-hydroxy-tetrahydrodipicolinate synthase | ||||||||||||
Keywords | LYASE / DHDPS / Lysine biosynthesis / tetramer | ||||||||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å | ||||||||||||
Authors | Impey, R.E. / Lee, M. / Hawkins, D.A. / Sutton, J.M. / Panjikar, S. / Perugini, M.A. / Soares da Costa, T.P. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Febs Lett. / Year: 2020 Title: Mis-annotations of a promising antibiotic target in high-priority gram-negative pathogens. Authors: Impey, R.E. / Lee, M. / Hawkins, D.A. / Sutton, J.M. / Panjikar, S. / Perugini, M.A. / Soares da Costa, T.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ue0.cif.gz | 138 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ue0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ue0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ue0_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 6ue0_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 6ue0_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 6ue0_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/6ue0 ftp://data.pdbj.org/pub/pdb/validation_reports/ue/6ue0 | HTTPS FTP |
-Related structure data
Related structure data | 1yxcS 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: 34816.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: dapA_2, dapA_3, dapA_4, dapA_5, dapA_6, dapA_7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: W9BBZ5, 4-hydroxy-tetrahydrodipicolinate synthase #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris, ph 7.5, 2 M Ammonium Sulfate, 5 mM Pyruvate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→49.039 Å / Num. obs: 54112 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.89→1.93 Å / Num. unique obs: 3259 / CC1/2: 0.827 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YXC Resolution: 1.892→48.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.582 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.117 Details: Hydrogens have been added in their 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: 22.372 Å2
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Refinement step | Cycle: LAST / Resolution: 1.892→48.99 Å
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Refine LS restraints |
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LS refinement shell |
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