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Yorodumi- PDB-4mu3: The form A structure of an E21Q catalytic mutant of A. thaliana I... -
+Open data
-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 | ||||||
Components | Imidazoleglycerol-phosphate dehydratase 2, chloroplastic | ||||||
Keywords | LYASE/LYASE INHIBITOR / hydro-lyase / histidine biosynthesis / manganese binding / chloroplastic / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | Function and homology information imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / chloroplast / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Bisson, C. / Britton, K.L. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W. | ||||||
Citation | Journal: Structure / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mu3.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mu3.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/4mu3 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/4mu3 | HTTPS FTP |
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-Related structure data
Related structure data | 4mu0C 4mu1C 4mu4C 4qnjC 4qnkC 2f1dS 4mu2 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Arabidopsis thaliana (thale cress) / Gene: At4g14910, dl3495c, HISN5B / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase |
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-Non-polymers , 5 types, 214 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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