+Open data
-Basic information
Entry | Database: PDB / ID: 7t34 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AtDHDPR1 from Arabidopsis thaliana | ||||||
Components | 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic | ||||||
Keywords | PLANT PROTEIN / dihydrodipicolinate reductase / DHDPR / Arabidopsis thaliana | ||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / chloroplast stroma / lysine biosynthetic process via diaminopimelate / NADPH binding / chloroplast / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Mackie, E.R.R. / Panjikar, S. / Soares da Costa, T.P. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: To be published Title: From bacteria to plants: a repurposing strategy in the pursuit for novel herbicides Authors: Mackie, E.R.R. / Barrow, A.S. / Giel, M.C. / Hulett, M.D. / Gendall, A.R. / Panjikar, S. / Soares da Costa, T.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7t34.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7t34.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 7t34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/7t34 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/7t34 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1arzS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32274.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DAPB1, At2g44040, F6E13.17 / Production host: Escherichia coli (E. coli) References: UniProt: O80574, 4-hydroxy-tetrahydrodipicolinate reductase |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M bis-tris hydrochloride (pH 6.5), 0.245 M magnesium formate, 22% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2021 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.889→49.05 Å / Num. obs: 11082 / % possible obs: 99.68 % / Redundancy: 13.09 % / Biso Wilson estimate: 116.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.046 / Net I/σ(I): 30.28 |
Reflection shell | Resolution: 2.889→2.993 Å / Rmerge(I) obs: 0.1197 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 11082 / CC1/2: 0.846 / Rrim(I) all: 0.1244 / % possible all: 97.74 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ARZ Resolution: 2.89→49.05 Å / SU ML: 0.4003 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7357 / Stereochemistry target values: GeoStd + Monomer Library
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→49.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|