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- PDB-3k9q: Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k9q | ||||||
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Title | Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 from Methicillin resistant Staphylococcus aureus (MRSA252) at 2.5 angstrom resolution | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / Glycolysis / NAD | ||||||
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 | ![]() | 270.4 KB | Display | ![]() |
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PDB format | ![]() | 219.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hq4C ![]() 3k73C ![]() 3ksdC ![]() 3kszC ![]() 3kv3C ![]() 3l4sC ![]() 3l6oC ![]() 3lc1C ![]() 3lc2C ![]() 3lc7C ![]() 3lvfC ![]() 3h48 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 1 - 335 / Label seq-ID: 1 - 335
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Components
#1: Protein | Mass: 36274.672 Da / Num. of mol.: 4 / Mutation: C151G 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 | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.27 % / Mosaicity: 0.389 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M TRIS-HCl pH8.2, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2009 / Details: 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: 2.5→86.57 Å / Num. obs: 42157 / % possible obs: 100 % / Redundancy: 3.72 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1 / Net I/σ(I): 9.9 / Scaling rejects: 1187 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.7 / Num. measured all: 14800 / Num. unique all: 4213 / Χ2: 1.23 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H48 ![]() 3h48 Resolution: 2.5→27.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.861 / SU B: 19.79 / SU ML: 0.205 / SU R Cruickshank DPI: 0.243 / SU Rfree: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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: 59.17 Å2 / Biso mean: 23.495 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→27.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 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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