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- PDB-4l8w: Crystal structure of gamma glutamyl hydrolase (H218N) from zebraf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l8w | ||||||
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Title | Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with MTX polyglutamate | ||||||
![]() | Gamma-glutamyl hydrolase | ||||||
![]() | HYDROLASE / Sandwiched-like domain | ||||||
Function / homology | ![]() folate gamma-glutamyl hydrolase / tetrahydrofolylpolyglutamate metabolic process / gamma-glutamyl-peptidase activity / Neutrophil degranulation / folic acid-containing compound metabolic process / vacuole / glutamine metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chuankhayan, P. / Kao, T.-T. / Chen, C.-J. / Fu, T.-F. | ||||||
![]() | ![]() Title: Structural insights into the hydrolysis and polymorphism of methotrexate polyglutamate by zebrafish gamma-glutamyl hydrolase Authors: Chuankhayan, P. / Kao, T.-T. / Lin, C.-C. / Guan, H.-H. / Nakagawa, A. / Fu, T.-F. / Chen, C.-J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354 KB | Display | ![]() |
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PDB format | ![]() | 289.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 68.5 KB | Display | |
Data in CIF | ![]() | 93.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l7qC ![]() 4l8fC ![]() 4l8yC ![]() 4l95C ![]() 1l9xS 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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Unit cell |
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Components
#1: Protein | Mass: 35392.918 Da / Num. of mol.: 6 / Mutation: H218N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6NY42, folate gamma-glutamyl hydrolase #2: Chemical | #3: Chemical | ChemComp-DGL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 3350, 8% Tassimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 10, 2012 |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→30 Å / Num. all: 82119 / Num. obs: 82119 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.39→2.47 Å / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1L9X Resolution: 2.39→29.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.831 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.27 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.789 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.386→2.448 Å / Total num. of bins used: 20
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