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- PDB-7d96: Crystal structure of D110G mutant of GATase subunit of Methanocal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d96 | |||||||||
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Title | Crystal structure of D110G mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase | |||||||||
![]() | GMP synthase [glutamine-hydrolyzing] subunit A | |||||||||
![]() | LIGASE / Deamidation / hyperthermostable glutamine amidotransferase / GATase_D110G | |||||||||
Function / homology | ![]() GMP synthase activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bellur, A. / Dongre, A. / Aggarwal, R. / Balaram, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Authors: Dongre, A.V. / Das, S. / Bellur, A. / Kumar, S. / Chandrashekarmath, A. / Karmakar, T. / Balaram, P. / Balasubramanian, S. / Balaram, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.4 KB | Display | ![]() |
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Full document | ![]() | 429.4 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d40SC ![]() 7d95C ![]() 7d97C S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 20993.213 Da / Num. of mol.: 1 / Mutation: D110G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 2661 / Gene: guaAA, MJ1575 / Production host: ![]() ![]() References: UniProt: Q58970, GMP synthase (glutamine-hydrolysing) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 5.6 / Details: 100 mM Sodium acetate, pH 5.6, 10 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50.99 Å / Num. obs: 8066 / % possible obs: 89.3 % / Redundancy: 4.7 % / CC1/2: 0.97 / Net I/σ(I): 4.02 |
Reflection shell | Resolution: 2.29→2.41 Å / Num. unique obs: 1258 / CC1/2: 0.881 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D40 Resolution: 2.29→50.99 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.847 / SU B: 8.639 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 52.76 Å2 / Biso mean: 17.09 Å2 / Biso min: 4.94 Å2
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Refinement step | Cycle: final / Resolution: 2.29→50.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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