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- PDB-3uwz: Crystal structure of Staphylococcus aureus triosephosphate isomer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uwz | ||||||
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Title | Crystal structure of Staphylococcus aureus triosephosphate isomerase complexed with glycerol-2-phosphate | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / TIM BARREL / CYTOSOL | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mukherjee, S. / Roychowdhury, A. / Dutta, D. / Das, A.K. | ||||||
![]() | ![]() Title: Crystal structures of triosephosphate isomerase from methicillin resistant Staphylococcus aureus MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop Authors: Mukherjee, S. / Roychowdhury, A. / Dutta, D. / 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 | ![]() | 111.5 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m9ySC ![]() 3uwuC ![]() 3uwvC ![]() 3uwwC ![]() 3uwyC 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: Ens-ID: 1 / Refine code: 2
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Components
#1: Protein | Mass: 28264.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M TRISODIUM CITRATE, pH 6.5, 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: Sep 26, 2010 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.497→72.017 Å / Num. obs: 19971 / % possible obs: 99.5 % / Redundancy: 14 % / Rsym value: 0.086 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.5→2.63 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.524 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3M9Y Resolution: 2.5→29.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.592 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.571 / ESU R Free: 0.273 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.56 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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