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- PDB-6vvi: Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vvi | ||||||
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Title | Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) | ||||||
![]() | 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic | ||||||
![]() | LYASE / Dihydrodipicolinate Synthase | ||||||
Function / homology | ![]() 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / chloroplast Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, M. / Hall, C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms. Authors: Hall, C.J. / Lee, M. / Boarder, M.P. / Mangion, A.M. / Gendall, A.R. / Panjikar, S. / Perugini, M.A. / Soares da Costa, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 275.5 KB | Display | ![]() |
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Full document | ![]() | 276.5 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vvhC ![]() 4dppS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35539.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9LZX6, 4-hydroxy-tetrahydrodipicolinate synthase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.5), 0.1 M NaCl, and 1.4 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→49.1 Å / Num. obs: 90994 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.14→2.2 Å / Num. unique obs: 4163 / CC1/2: 0.865 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DPP Resolution: 2.145→49.098 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.617 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.157 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: 40.455 Å2
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Refinement step | Cycle: LAST / Resolution: 2.145→49.098 Å
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Refine LS restraints |
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LS refinement shell |
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