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Yorodumi- PDB-4l95: Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l95 | ||||||
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Title | Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish | ||||||
Components | Gamma-glutamyl hydrolase | ||||||
Keywords | HYDROLASE / Sandwiched-like domain | ||||||
Function / homology | Function and homology information 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 | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Chuankhayan, P. / Kao, T.-T. / Chen, C.-J. / Fu, T.-F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l95.cif.gz | 345.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l95.ent.gz | 283 KB | Display | PDB format |
PDBx/mmJSON format | 4l95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l95_validation.pdf.gz | 498.6 KB | Display | wwPDB validaton report |
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Full document | 4l95_full_validation.pdf.gz | 556.9 KB | Display | |
Data in XML | 4l95_validation.xml.gz | 66.6 KB | Display | |
Data in CIF | 4l95_validation.cif.gz | 90.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/4l95 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l95 | HTTPS FTP |
-Related structure data
Related structure data | 4l7qC 4l8fC 4l8wC 4l8yC 1l9xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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.) Danio rerio (zebrafish) / Gene: ggh / Production host: Escherichia coli (E. coli) References: UniProt: Q6NY42, folate gamma-glutamyl hydrolase #2: Chemical | #3: 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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10%(w/v) PEG 8000, 0.2M NaCl, 0.1M Na/K buffer, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 25, 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: 2.34→30 Å / Num. all: 88182 / Num. obs: 88182 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.34→2.42 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L9X Resolution: 2.34→29.76 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.656 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.299 / 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: 50.285 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.34→2.401 Å / Total num. of bins used: 20
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