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- PDB-3lc2: Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lc2 | ||||||
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Title | Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant Staphylococcus aureus MRSA252 | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase 1![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() 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 | ![]() | 260.6 KB | Display | ![]() |
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PDB format | ![]() | 211.8 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 ![]() 3k9qC ![]() 3ksdC ![]() 3kszC ![]() 3kv3C ![]() 3l4sC ![]() 3l6oC ![]() 3lc1C ![]() 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 2 - 334 / Label seq-ID: 2 - 334
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Components
#1: Protein | ![]() Mass: 36320.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q6GIL8, ![]() #2: Chemical | ChemComp-G3H / ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.02 % / Mosaicity: 0 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 32% (w/v) PEG 3350 , 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: Dec 19, 2009 / Details: Varimax mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.793→85.178 Å / Num. all: 29489 / Num. obs: 29489 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.134 |
Reflection shell | Resolution: 2.79→2.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4196 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3H48 ![]() 3h48 Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.152 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.853 / SU B: 33.943 / SU ML: 0.299 / SU R Cruickshank DPI: 0.315 / SU Rfree: 0.417 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.61 Å2 / Biso mean: 37.376 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2523 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.871 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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