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- PDB-4mu3: The form A structure of an E21Q catalytic mutant of A. thaliana I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mu3 | ||||||
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Title | The form A structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and a mixture of its substrate, 2R3S-IGP, and an inhibitor, 2S3S-IGP, to 1.12 A resolution | ||||||
![]() | Imidazoleglycerol-phosphate dehydratase 2, chloroplastic | ||||||
![]() | LYASE/LYASE INHIBITOR / hydro-lyase / histidine biosynthesis / manganese binding / chloroplastic / LYASE-LYASE INHIBITOR complex | ||||||
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. / Baker, P.J. / Rice, D.W. | ||||||
![]() | ![]() Title: Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination. 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 | ![]() | 100.7 KB | Display | ![]() |
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PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mu0C ![]() 4mu1C ![]() 4mu4C ![]() 4qnjC ![]() 4qnkC ![]() 2f1dS ![]() 4mu2 C: citing same article ( S: Starting model for refinement |
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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: 22390.143 Da / Num. of mol.: 1 / Fragment: short construct (UNP residues 69-272) / Mutation: E21Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase |
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-Non-polymers , 5 types, 214 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/IG2.gif)
![](data/chem/img/IYP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IG2.gif)
![](data/chem/img/IYP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-IG2 / ( | #4: Chemical | ChemComp-IYP / ( | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2011 / Details: Kirkpatrick Baez bimorph mirror pair |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→46.17 Å / Num. all: 94992 / Num. obs: 94992 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.5 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F1D Resolution: 1.12→46.17 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.568 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / 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: 16.019 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→46.17 Å
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Refine LS restraints |
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