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Yorodumi- PDB-7xlo: Crystal Structure of the Catalytic Domain of Inosine Monophosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xlo | |||||||||
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Title | Crystal Structure of the Catalytic Domain of Inosine Monophosphate Dehydrogenase (IMPDH) from Methanocaldococcus jannaschii | |||||||||
Components | Inosine-5'-monophosphate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / IMPDH TIM / Catalytic domain / alpha and beta proteins (a/b) / TIM beta/alpha-barrel | |||||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Bellur, A. / Sharma, P. / Balaram, H. | |||||||||
Funding support | India, 2items
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Citation | Journal: To Be Published Title: Crystal Structure of the Catalytic Domain of Inosine Monophosphate Dehydrogenase (IMPDH) from Methanocaldococcus jannaschii Authors: Bellur, A. / Sharma, P. / Balaram, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xlo.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xlo.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/7xlo ftp://data.pdbj.org/pub/pdb/validation_reports/xl/7xlo | HTTPS FTP |
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-Related structure data
Related structure data | 2cu0S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42253.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: guaB, MJ1616 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59011, IMP dehydrogenase #2: 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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 297 K / Method: microbatch Details: 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 30% v/v polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 31, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→53.37 Å / Num. obs: 24178 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.845 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.6→2.74 Å / Num. unique obs: 24178 / CC1/2: 0.845 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2cu0 Resolution: 2.6→53.37 Å / Cor.coef. Fo:Fc: 0.827 / Cor.coef. Fo:Fc free: 0.806 / SU B: 15.822 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.339 / 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: 15.675 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→53.37 Å
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