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Yorodumi- PDB-5ibx: 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ibx | ||||||
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Title | 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae | ||||||
Components | (Triosephosphate isomerase) x 2 | ||||||
Keywords | ISOMERASE / triosephosphate isomerase / tpiA / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae serotype 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ibx.cif.gz | 798.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ibx.ent.gz | 664.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ibx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ibx_validation.pdf.gz | 491.9 KB | Display | wwPDB validaton report |
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Full document | 5ibx_full_validation.pdf.gz | 501.7 KB | Display | |
Data in XML | 5ibx_validation.xml.gz | 94.2 KB | Display | |
Data in CIF | 5ibx_validation.cif.gz | 142.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/5ibx ftp://data.pdbj.org/pub/pdb/validation_reports/ib/5ibx | HTTPS FTP |
-Related structure data
Related structure data | 3m9yS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 26923.432 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria) Strain: D39 / NCTC 7466 / Gene: tpiA, SPD_1404 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q04JH4, triose-phosphate isomerase #2: Protein | Mass: 26847.314 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria) Strain: D39 / NCTC 7466 / Gene: tpiA, SPD_1404 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q04JH4, triose-phosphate isomerase #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 7.5mg/ml, 0.25M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME; Screen: Classics II(F12), 0.2M Sodium chloride, 0.1M HEPES (pH 7.5), 25%(w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2014 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 225519 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 20.1 Å2 / CC1/2: 0.757 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.3 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M9Y Resolution: 1.65→29.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.87 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.805 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→29.69 Å
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