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Yorodumi- PDB-3k9q: Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate d... -
+Open data
-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 | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase 1Glyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / Glycolysis / NAD | ||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k9q.cif.gz | 270.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k9q.ent.gz | 219.7 KB | Display | PDB format |
PDBx/mmJSON format | 3k9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/3k9q ftp://data.pdbj.org/pub/pdb/validation_reports/k9/3k9q | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: gap, gap1, gapA, gapA1, SAR0828 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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