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- PDB-4unl: Crystal structure of a single mutant (N71D) of triosephosphate is... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4unl | ||||||
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Title | Crystal structure of a single mutant (N71D) of triosephosphate isomerase from human | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE / DEAMIDATION | ||||||
Function / homology | ![]() methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / glycerol catabolic process / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / glycerol catabolic process / Glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | DeLaMora-DeLaMora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / Garcia-Torres, I. ...DeLaMora-DeLaMora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / Garcia-Torres, I. / Reyes-Vivas, H. / Oria-Hernandez, J. | ||||||
![]() | ![]() Title: Crystal Structure of a Single Mutant (N71D) of Triosephosphate Isomerase from Human Authors: Delamora-Delamora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / ...Authors: Delamora-Delamora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / Garcia-Torres, I. / Reyes-Vivas, H. / Oria-Hernandez, J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 431.4 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jk2S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8199, 0.2977, 0.489), Vector: |
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Components
#1: Protein | Mass: 26571.254 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-286 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.67 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: PROTEIN WAS CRYSTALLIZED FROM: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4,000 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 28, 2010 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.28 Å / Num. obs: 71346 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JK2 Resolution: 1.5→39.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.537 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→39.28 Å
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Refine LS restraints |
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