+Open data
-Basic information
Entry | Database: PDB / ID: 4uoy | ||||||
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Title | Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate | ||||||
Components | PUTRESCINE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å | ||||||
Authors | Jeong, J.H. / Kim, Y.G. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases. Authors: Cha, H.J. / Jeong, J. / Rojviriya, C. / Kim, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uoy.cif.gz | 345.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uoy.ent.gz | 282.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uoy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uoy_validation.pdf.gz | 497.5 KB | Display | wwPDB validaton report |
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Full document | 4uoy_full_validation.pdf.gz | 511.9 KB | Display | |
Data in XML | 4uoy_validation.xml.gz | 63.9 KB | Display | |
Data in CIF | 4uoy_validation.cif.gz | 88.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uoy ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uoy | HTTPS FTP |
-Related structure data
Related structure data | 4uoxC 1vefS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50785.324 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: COVALENT BOND BETWEEN K 300 AND PYRIDOXAL-5'-PHOSPHATE Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B84(DE3) References: UniProt: P42588, putrescine-2-oxoglutarate transaminase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-FMT / | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY | |
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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: 2.58 Å3/Da / Density % sol: 52.44 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5 15% PEG 3350 0.2 M SODIUM FORMATE 0.1 MM N-DODECYL-N,N-DIMETHYLGLYCINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 91029 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 23.17 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VEF Resolution: 2.305→29.746 Å / SU ML: 0.34 / σ(F): 1.49 / Phase error: 21.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.305→29.746 Å
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Refine LS restraints |
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LS refinement shell |
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