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Yorodumi- PDB-7loy: Dihydrodipicolinate synthase with pyruvate from Candidatus Liberi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7loy | |||||||||
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Title | Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum | |||||||||
Components | 4-hydroxy-tetrahydrodipicolinate synthaseDihydrodipicolinate synthase | |||||||||
Keywords | LYASE / TIM Barrel | |||||||||
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 | Candidatus Liberibacter solanacearum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J. | |||||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearum Authors: Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7loy.cif.gz | 340.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7loy.ent.gz | 277.3 KB | Display | PDB format |
PDBx/mmJSON format | 7loy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/7loy ftp://data.pdbj.org/pub/pdb/validation_reports/lo/7loy | HTTPS FTP |
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-Related structure data
Related structure data | 8gekC 4i7uS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 31879.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Liberibacter solanacearum (bacteria) Gene: dapA / Plasmid: pGRO7 Details (production host): GroEL/GroES chaperone co-expression Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0F4VK59 #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3000, 0.1 M sodium citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953723 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953723 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.32 Å / Num. obs: 79992 / % possible obs: 99.82 % / Redundancy: 4 % / CC1/2: 0.917 / Net I/σ(I): 1.04 |
Reflection shell | Resolution: 2.4→2.486 Å / Num. unique obs: 79992 / CC1/2: 0.702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4I7U Resolution: 2.4→46.27 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.132 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.263 / 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: 35.948 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→46.27 Å
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Refine LS restraints |
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