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Yorodumi- PDB-7yc6: Crystal structure of D110P mutant of GATase subunit of Methanocal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yc6 | |||||||||
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Title | Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase | |||||||||
Components | GMP synthase [glutamine-hydrolyzing] subunit A | |||||||||
Keywords | TRANSFERASE / amidotransferase / succinimide / deamidation / thermostability | |||||||||
Function / homology | Function and homology information GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Chandrashekarmath, A. / Bellur, A. | |||||||||
Funding support | India, 2items
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Citation | Journal: To Be Published Title: Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase Authors: Chandrashekarmath, A. / Bellur, A. / Balaram, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yc6.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yc6.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/7yc6 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/7yc6 | HTTPS FTP |
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-Related structure data
Related structure data | 7d40S 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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Unit cell |
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-Components
#1: Protein | Mass: 21033.277 Da / Num. of mol.: 1 / Mutation: D110P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58970 | ||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.12 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / Details: 0.2M Zinc acetate dihydrate, 20% PEG 3350, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→54.63 Å / Num. obs: 9659 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Num. unique obs: 9659 / CC1/2: 0.995 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D40 Resolution: 2.4→54.63 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.215 / 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: 15.67 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→54.63 Å
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Refine LS restraints |
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