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Yorodumi- PDB-4hg3: Structural insights into yeast Nit2: wild-type yeast Nit2 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hg3 | ||||||
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Title | Structural insights into yeast Nit2: wild-type yeast Nit2 in complex with alpha-ketoglutarate | ||||||
Components | Probable hydrolase NIT2 | ||||||
Keywords | HYDROLASE / nitrilase superfamily / omega-amidase | ||||||
Function / homology | Function and homology information deaminated glutathione amidase / [acetyl-CoA carboxylase]-phosphatase activity / deaminated glutathione amidase activity / amide catabolic process / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Liu, H. / Qiu, X. / Zhang, M. / Gao, Y. / Niu, L. / Teng, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2 Authors: Liu, H. / Gao, Y. / Zhang, M. / Qiu, X. / Cooper, A.J.L. / Niu, L. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hg3.cif.gz | 261.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hg3.ent.gz | 208.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hg3_validation.pdf.gz | 509.3 KB | Display | wwPDB validaton report |
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Full document | 4hg3_full_validation.pdf.gz | 524.5 KB | Display | |
Data in XML | 4hg3_validation.xml.gz | 51 KB | Display | |
Data in CIF | 4hg3_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hg3 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hg3 | HTTPS FTP |
-Related structure data
Related structure data | 4h5uSC 4hg5C 4hgdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38293.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: NIT2, YJL126W, J0706 / Production host: Escherichia coli (E. coli) References: UniProt: P47016, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds #2: Chemical | ChemComp-AKG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CAC / #5: 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: 2.08 Å3/Da / Density % sol: 40.76 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 17.5% PEG4000, 0.1M sodium cacodylate, 25mM 2-oxoglutaric acid sodium salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 92926 / Num. obs: 92897 / % possible obs: 100 % / Observed criterion σ(I): 2.6 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H5U Resolution: 1.93→48.84 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.54 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.153 / 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: 13.966 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→48.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.984 Å / Total num. of bins used: 20
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