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- PDB-4mu0: The structure of wt A. thaliana IGPD2 in complex with Mn2+ and 1,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mu0 | ||||||
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Title | The structure of wt A. thaliana IGPD2 in complex with Mn2+ and 1,2,4-triazole at 1.3 A resolution | ||||||
![]() | Imidazoleglycerol-phosphate dehydratase 2, chloroplastic | ||||||
![]() | LYASE / hydro-lyase / histidine biosynthesis / manganese binding / chloroplastic | ||||||
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 | ![]() | 96.1 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 445.8 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mu1C ![]() 4mu3C ![]() 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: 22391.127 Da / Num. of mol.: 1 / Fragment: short construct (UNP residues 69-272) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase |
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-Non-polymers , 6 types, 155 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/TRI.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRI.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-TRI / | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: 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: 54.35 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30% PEG200, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011 / Details: two K-B pairs of bimorph type mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50.59 Å / Num. all: 61097 / Num. obs: 61097 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 12.36 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4421 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F1D Resolution: 1.3→50.59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.896 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.033 / 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: 19.128 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→50.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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