[English] 日本語
Yorodumi- PDB-3ff3: The high resolution structure of human glutamate carboxypeptidase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ff3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The high resolution structure of human glutamate carboxypeptidase III (GCPIII/NAALADase II) in complex with L-glutamate | |||||||||
Components | Glutamate carboxypeptidase III | |||||||||
Keywords | HYDROLASE / metallopeptidase / bimetallic active site / N-glycosylation / calcium cation / chloride anion / zinc ions / Carboxypeptidase / Dipeptidase / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Multifunctional enzyme / Protease / Signal-anchor / Transmembrane | |||||||||
Function / homology | Function and homology information glutamate carboxypeptidase II / Aspartate and asparagine metabolism / dipeptidase activity / dipeptidyl-peptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / serine-type peptidase activity / proteolysis / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.37 Å | |||||||||
Authors | Lubkowski, J. / Barinka, C. | |||||||||
Citation | Journal: Febs J. / Year: 2009 Title: Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III Authors: Hlouchova, K. / Barinka, C. / Konvalinka, J. / Lubkowski, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ff3.cif.gz | 349.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ff3.ent.gz | 279.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ff3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ff3_validation.pdf.gz | 855.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ff3_full_validation.pdf.gz | 876.2 KB | Display | |
Data in XML | 3ff3_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 3ff3_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/3ff3 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/3ff3 | HTTPS FTP |
-Related structure data
Related structure data | 3fecC 3fedSC 3feeC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79940.578 Da / Num. of mol.: 1 / Fragment: Extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAALAD2 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: Q9Y3Q0, glutamate carboxypeptidase II |
---|
-Sugars , 2 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar |
-Non-polymers , 6 types, 989 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-GLU / | #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES-Na, 10% (w/v) PEG6000, 5% (v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→20 Å / Num. all: 189722 / Num. obs: 189722 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 1.37→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2 / Num. unique all: 17742 / % possible all: 92 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3FED Resolution: 1.37→19.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.333 / SU ML: 0.024 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.298 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→19.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.37→1.405 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 19.356 Å / Origin y: 45.926 Å / Origin z: 13.359 Å
|