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Yorodumi- PDB-1yw6: Crystal Structure of Succinylglutamate Desuccinylase from Escheri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yw6 | ||||||
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Title | Crystal Structure of Succinylglutamate Desuccinylase from Escherichia coli, Northeast Structural Genomics Target ET72. | ||||||
Components | Succinylglutamate desuccinylase | ||||||
Keywords | HYDROLASE / alpha-beta protein. / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information succinylglutamate desuccinylase / succinylglutamate desuccinylase activity / arginine catabolic process to succinate / arginine catabolic process to glutamate / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å | ||||||
Authors | Forouhar, F. / Yong, W. / Kuzin, A.P. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Succinylglutamate Desuccinylase from Escherichia coli, Northeast Structural Genomics Target ET72. Authors: Forouhar, F. / Yong, W. / Kuzin, A.P. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yw6.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yw6.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yw6_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 1yw6_full_validation.pdf.gz | 485.9 KB | Display | |
Data in XML | 1yw6_validation.xml.gz | 28 KB | Display | |
Data in CIF | 1yw6_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/1yw6 ftp://data.pdbj.org/pub/pdb/validation_reports/yw/1yw6 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37806.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: astE / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic Keywords: Substitution of Met by Seleno-Met and addition of five residues at N-terminus (MAGDP) and a C-tag (LEHHHHHH), AstE References: UniProt: P76215, Hydrolases; Acting on ester bonds #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: 3.94 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl (pH 8.0), 1.5 M magnesium sulfate, and DTT., VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926, 0.97949, 0.94644 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 11, 2005 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.1→30 Å / Num. all: 39627 / Num. obs: 39469 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.094 / Net I/σ(I): 21.25 | ||||||||||||
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3950 / Rsym value: 0.687 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.1→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 266586.28 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9776 Å2 / ksol: 0.340631 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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