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- PDB-4mu1: The structure of wt A. thaliana IGPD2 in complex with Mn2+, imida... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mu1 | ||||||
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Title | The structure of wt A. thaliana IGPD2 in complex with Mn2+, imidazole, and sulfate at 1.5 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 | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.2 KB | Display | ![]() |
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Full document | ![]() | 447.2 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mu0C ![]() 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: 23683.463 Da / Num. of mol.: 1 / Fragment: long construct (UNP residues 54-272) 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, 224 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-IMD / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG3000, 0.2 M lithium sulfate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING 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: Mar 11, 2008 / 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: 0.9507 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40.26 Å / Num. all: 40587 / Num. obs: 40587 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 12.651 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 4 / Num. unique all: 2956 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2F1D Resolution: 1.5→40.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.874 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.061 / 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: 22.688 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40.26 Å
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Refine LS restraints |
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