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Yorodumi- PDB-3k7o: Structure of type B ribose 5-phosphate isomerase from Trypanosoma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k7o | ||||||
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Title | Structure of type B ribose 5-phosphate isomerase from Trypanosoma cruzi | ||||||
Components | Ribose 5-phosphate isomerase | ||||||
Keywords | ISOMERASE / pentose phosphate pathway / Type B ribose 5-phosphate isomerase (RpiB) / R5P | ||||||
Function / homology | Function and homology information isomerase activity / carbohydrate metabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Naworyta, A. / Mowbray, S.L. / Stern, A.L. | ||||||
Citation | Journal: Febs J. / Year: 2011 Title: Structures of type B ribose 5-phosphate isomerase from Trypanosoma cruzi shed light on the determinants of sugar specificity in the structural family. Authors: Stern, A.L. / Naworyta, A. / Cazzulo, J.J. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k7o.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k7o.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 3k7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/3k7o ftp://data.pdbj.org/pub/pdb/validation_reports/k7/3k7o | HTTPS FTP |
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-Related structure data
Related structure data | 3k7pSC 3k7sC 3k8cC 3m1pC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19559.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: strain CL Brener / Gene: 110984573 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: A1BTJ7, UniProt: Q4CQE2*PLUS, ribose-5-phosphate isomerase #2: 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: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.5% (v/v) Jeffamine ED-2001, 0.1M HEPES, 1.1 M Na-malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→66.082 Å / Num. obs: 28418 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.2 / Num. measured all: 20502 / Num. unique all: 4075 / Rsym value: 0.641 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K7P Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.861 / SU B: 3.496 / SU ML: 0.098 / SU R Cruickshank DPI: 0.16 / SU Rfree: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.142 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.16 Å2 / Biso mean: 31.092 Å2 / Biso min: 16.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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