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- PDB-3k8c: Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k8c | ||||||
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Title | Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with 4-deoxy-4-phospho-D-erythronohydroxamic acid | ||||||
![]() | Ribose 5-phosphate isomerase | ||||||
![]() | ISOMERASE / pentose phosphate pathway / Type B ribose 5-phosphate isomerase (RpiB) / 4PEH / 4-deoxy-4-phospho-D-erythronohydroxamic acid | ||||||
Function / homology | ![]() isomerase activity / carbohydrate metabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naworyta, A. / Mowbray, S.L. / Stern, A.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.6 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k7oC ![]() 3k7pSC ![]() 3k7sC ![]() 3m1pC 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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1 | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() ![]() References: UniProt: A1BTJ7, UniProt: Q4CQE2*PLUS, ribose-5-phosphate isomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% (w/v) PEG 6000, 0.2 M ammonium chloride, 0.1 M Tris-HCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→65.938 Å / Num. obs: 23175 / % possible obs: 96 % / Observed criterion σ(F): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.451 / % possible all: 95.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K7P Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.474 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 1.579 / ESU R Free: 0.185 / 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 mean: 21.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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