+Open data
-Basic information
Entry | Database: PDB / ID: 4xwu | ||||||
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Title | Structure of the IMP dehydrogenase from Ashbya gossypii | ||||||
Components | Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / IMP dehydrogenase / Ashbya gossypii | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Ashbya gossypii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Buey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2015 Title: Increased riboflavin production by manipulation of inosine 5'-monophosphate dehydrogenase in Ashbya gossypii. Authors: Buey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xwu.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xwu.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/4xwu ftp://data.pdbj.org/pub/pdb/validation_reports/xw/4xwu | HTTPS FTP |
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-Related structure data
Related structure data | 4xtdC 4xtiC 4avfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44528.555 Da / Num. of mol.: 1 / Fragment: UNP residues 1-119,UNP residues 236-522 Mutation: The CBS domain (residues 120-325) has been replaced by the sequence stretch SQDG. Residues numbered according to the full-length wild-type sequence,The CBS domain (residues 120-325) has ...Mutation: The CBS domain (residues 120-325) has been replaced by the sequence stretch SQDG. Residues numbered according to the full-length wild-type sequence,The CBS domain (residues 120-325) has been replaced by the sequence stretch SQDG. Residues numbered according to the full-length wild-type sequence Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus) Gene: AGOS_AER117W / Production host: Escherichia coli (E. coli) / References: UniProt: Q756Z6, IMP dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 40% PEG-300, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→39.39 Å / Num. obs: 39565 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.0397 / Net I/σ(I): 30.28 |
Reflection shell | Resolution: 1.75→1.813 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.88 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4avf Resolution: 1.75→39.39 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→39.39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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