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Yorodumi- PDB-4l7q: Crystal structure of gamma glutamyl hydrolase (wild-type) from ze... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l7q | ||||||
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Title | Crystal structure of gamma glutamyl hydrolase (wild-type) from zebrafish | ||||||
Components | Gamma-glutamyl hydrolase | ||||||
Keywords | HYDROLASE / sandwiched-like domains | ||||||
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: 2.1 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 | 4l7q.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l7q.ent.gz | 294.6 KB | Display | PDB format |
PDBx/mmJSON format | 4l7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l7q_validation.pdf.gz | 499.1 KB | Display | wwPDB validaton report |
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Full document | 4l7q_full_validation.pdf.gz | 542.6 KB | Display | |
Data in XML | 4l7q_validation.xml.gz | 72.5 KB | Display | |
Data in CIF | 4l7q_validation.cif.gz | 100.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/4l7q ftp://data.pdbj.org/pub/pdb/validation_reports/l7/4l7q | HTTPS FTP |
-Related structure data
Related structure data | 4l8fC 4l8wC 4l8yC 4l95C 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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Unit cell |
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-Components
#1: Protein | Mass: 35416.961 Da / Num. of mol.: 6 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 | ChemComp-GOL / #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: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 4000, 0.1M Sodium citarte tribasic, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.1→30 Å / Num. all: 117219 / Num. obs: 117219 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L9X Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.826 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.207 / Stereochemistry target values: Engh & Huber / 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: 30.993 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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