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Yorodumi- PDB-5dnl: Crystal structure of IGPD from Pyrococcus furiosus in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dnl | |||||||||
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Title | Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348 | |||||||||
Components | Imidazoleglycerol-phosphate dehydratase | |||||||||
Keywords | LYASE / Inhibitor / Complex / Dehydratase / Cytoplasmic | |||||||||
Function / homology | Function and homology information imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Pyrococcus furiosus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | |||||||||
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. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dnl.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dnl.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/5dnl ftp://data.pdbj.org/pub/pdb/validation_reports/dn/5dnl | HTTPS FTP |
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-Related structure data
Related structure data | 5dnxC 5ekwC 5el9C 5elwC 2f1dS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19764.807 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: hisB, PF1660 / Production host: Escherichia coli (E. coli) References: UniProt: P58880, imidazoleglycerol-phosphate dehydratase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES buffer pH 6 and 10% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→49.25 Å / Num. obs: 103816 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.53→1.57 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F1D Resolution: 1.53→49.25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.777 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / 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: 19.679 Å2
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Refinement step | Cycle: 1 / Resolution: 1.53→49.25 Å
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Refine LS restraints |
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