[English] 日本語
![](img/lk-miru.gif)
- PDB-3ksd: Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ksd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.2 angstrom resolution | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 510.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 424.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 54 KB | Display | |
Data in CIF | ![]() | 73.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hq4C ![]() 3k73C ![]() 3k9qC ![]() 3kszC ![]() 3kv3C ![]() 3l4sC ![]() 3l6oC ![]() 3lc1C ![]() 3lc2C ![]() 3lc7C ![]() 3lvfC ![]() 3h48 S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
Components
#1: Protein | Mass: 36280.656 Da / Num. of mol.: 4 / Mutation: C151S, H178N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: MRSA252 / Gene: gap, gap1, gapA, gapA1, SAR0828 / Plasmid: pQE30 / Production host: ![]() ![]() References: UniProt: Q6GIL8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.84 % / Mosaicity: 0.746 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl pH8.5, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 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: 2.2→84.56 Å / Num. obs: 47907 / % possible obs: 90.1 % / Redundancy: 2.41 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.96 / Net I/σ(I): 9.6 / Scaling rejects: 874 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.9 / Num. measured all: 10947 / Num. unique all: 4906 / Χ2: 1.19 / % possible all: 93.2 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3H48 ![]() 3h48 Resolution: 2.2→25.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / SU B: 15.875 / SU ML: 0.195 / SU R Cruickshank DPI: 0.889 / SU Rfree: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.889 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 61.63 Å2 / Biso mean: 38.235 Å2 / Biso min: 2 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→25.84 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|