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- PDB-4ymz: DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ymz | ||||||
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Title | DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM) | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / TIM BARRELS / BETA-ALPHA BARRELS / DIHYDROXYACETONE PHOSPHATE / GLYCOLYSIS | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Pareek, V. / Balaram, P. / Murthy, M.R.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme Authors: Pareek, V. / Samanta, M. / Joshi, N.V. / Balaram, H. / Murthy, M.R.N. / Balaram, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.2 KB | Display | ![]() |
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Full document | ![]() | 476.1 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x22SC ![]() 4ywiC ![]() 4yxgC ![]() 4z0jC ![]() 4z0sC S: Starting model for refinement C: citing same article ( |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27340.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RGA / Gene: LEP2GSC113_RS0110880 / Plasmid: pTrc99A / Production host: ![]() ![]() References: UniProt: Q8F5I5*PLUS, triose-phosphate isomerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | The reference sequence database derived from str. RGA does not currently exist. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 16% PEG 8000, 1mM Ammonium sulfate, 10mM EDTA, 1mM Sodium azide, 100mM BIS/TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→56.75 Å / Num. all: 58862 / Num. obs: 54809 / % possible obs: 92.7 % / Redundancy: 11.8 % / Biso Wilson estimate: 22.8 Å2 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.87→1.97 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4X22 Resolution: 1.87→56.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.278 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / 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: 27.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→56.75 Å
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Refine LS restraints |
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