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- PDB-3ksz: Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ksz | ||||||
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Title | Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1) from Staphylococcus aureus MRSA252 complexed with NAD and G3P | ||||||
![]() | 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 | ![]() | 264.2 KB | Display | ![]() |
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PDB format | ![]() | 215.2 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 | ![]() | 51.5 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hq4C ![]() 3k73C ![]() 3k9qC ![]() 3ksdC ![]() 3kv3C ![]() 3l4sC ![]() 3l6oC ![]() 3lc1C ![]() 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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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 / Refine code: 2
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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: Chemical | ChemComp-3PG / #4: Water | ChemComp-HOH / | Nonpolymer details | THE 3PG IS NOT PHOSPHOGLYCERIC ACID STRUCTURALLY. THE LIGAND BOUND IS THE GEM DI-OL FORM OF ...THE 3PG IS NOT PHOSPHOGLY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.4 % / Mosaicity: 1.484 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris-HCl pH8.2, 24% 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: Nov 11, 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: 2.6→85.67 Å / Num. obs: 32754 / % possible obs: 99 % / Redundancy: 3.55 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.1 / Χ2: 0.96 / Net I/σ(I): 7.4 / Scaling rejects: 880 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.4 / Num. measured all: 9569 / Num. unique all: 2968 / Χ2: 1.16 / % possible all: 90.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H48 ![]() 3h48 Resolution: 2.6→33.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.83 / SU B: 28.854 / SU ML: 0.297 / SU R Cruickshank DPI: 0.309 / SU Rfree: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381 / 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: 92.7 Å2 / Biso mean: 51.081 Å2 / Biso min: 9.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→33.83 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: 2.6→2.667 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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