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- PDB-5elw: A. thaliana IGPD2 in complex with the triazole-phosphonate inhibi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5elw | ||||||
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Title | A. thaliana IGPD2 in complex with the triazole-phosphonate inhibitor, (R)-C348, to 1.36A resolution | ||||||
![]() | Imidazoleglycerol-phosphate dehydratase 2, chloroplastic | ||||||
![]() | LYASE / Herbicide development / Histidine biosynthesis / Inhibitor complex / Dehydratase | ||||||
Function / homology | ![]() imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / chloroplast / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bisson, C. / Britton, K.L. / Sedelnikova, S.E. / Rodgers, H.F. / Eadsforth, T.C. / Viner, R.C. / Hawkes, T.R. / Baker, P.J. / Rice, D.W. | ||||||
![]() | ![]() Title: Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Authors: Bisson, C. / Britton, K.L. / Sedelnikova, S.E. / Rodgers, H.F. / Eadsforth, T.C. / Viner, R.C. / Hawkes, T.R. / Baker, P.J. / Rice, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.6 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.9 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dnlC ![]() 5dnxC ![]() 5ekwSC ![]() 5el9C 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22391.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Construct B represents the mature polypeptide (residues 69-272), excluding an N-terminal signal sequence. No electron density was visible for the residues before S75, which was renumbered S9 ...Details: Construct B represents the mature polypeptide (residues 69-272), excluding an N-terminal signal sequence. No electron density was visible for the residues before S75, which was renumbered S9 for consistency with the structure of IGPD1 from A.thaliana (2F1D). Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase |
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-Non-polymers , 6 types, 211 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/5LD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5LD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-5LD / [( | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH8.5 and 20% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9802 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→45.96 Å / Num. all: 52156 / Num. obs: 52156 / % possible obs: 99 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.36→1.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / % possible all: 89.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EKW Resolution: 1.4→45.96 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.235 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.036 / 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: 11.722 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→45.96 Å
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Refine LS restraints |
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