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- PDB-3lc1: Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lc1 | ||||||
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Title | Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.0 angstrom resolution. | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / glycolysis | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K. | ||||||
![]() | ![]() Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism. Authors: Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268.8 KB | Display | ![]() |
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PDB format | ![]() | 217.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 73.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hq4C ![]() 3k73C ![]() 3k9qC ![]() 3ksdC ![]() 3kszC ![]() 3kv3C ![]() 3l4sC ![]() 3l6oC ![]() 3lc2C ![]() 3lc7C ![]() 3lvfC ![]() 3h48 C: citing same article ( S: Starting model for refinement |
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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: 36296.719 Da / Num. of mol.: 4 / Mutation: H178N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6GIL8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Mosaicity: 0.974 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris-HCl, pH 8.2, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2009 / Details: Varimax mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→86.82 Å / Num. obs: 80071 / % possible obs: 95.3 % / Redundancy: 3.73 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1 / Net I/σ(I): 9.9 / Scaling rejects: 2260 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.5 / Num. measured all: 28098 / Num. unique all: 7739 / Χ2: 1.25 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H48 ![]() 3h48 Resolution: 2→29.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 10.98 / SU ML: 0.141 / SU R Cruickshank DPI: 0.233 / SU Rfree: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.189 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.53 Å2 / Biso mean: 32.455 Å2 / Biso min: 10.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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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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