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Yorodumi- PDB-3m9y: Crystal structure of Triosephosphate isomerase from methicillin r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m9y | ||||||
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Title | Crystal structure of Triosephosphate isomerase from methicillin resistant Staphylococcus aureus at 1.9 Angstrom resolution | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM barrel / glycolysis / Gluconeogenesis / Pentose shunt | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K. | ||||||
Citation | Journal: Biochimie / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m9y.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m9y.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3m9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/3m9y ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m9y | HTTPS FTP |
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-Related structure data
Related structure data | 3uwuC 3uwvC 3uwwC 3uwyC 3uwzC 2btmS C: citing same article (ref.) S: Starting model for refinement |
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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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Components on special symmetry positions |
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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: 27378.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: SAR0830, tpi, tpiA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q6GIL6, triose-phosphate isomerase #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: 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: 2.52 Å3/Da / Density % sol: 51.26 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M TRISODIUM CITRATE DIHYDRATE, pH 6.5, 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: Oct 10, 2009 / Details: Varimax mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→72.365 Å / Num. all: 44961 / Num. obs: 44961 / % possible obs: 99.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6332 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BTM Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.881 / SU B: 6.189 / SU ML: 0.083 / SU R Cruickshank DPI: 0.127 / SU Rfree: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.2 Å2 / Biso mean: 31.097 Å2 / Biso min: 8.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 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: 1.9→1.949 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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