+Open data
-Basic information
Entry | Database: PDB / ID: 3niq | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa guanidinopropionase | ||||||
Components | 3-guanidinopropionase | ||||||
Keywords | HYDROLASE / guanidinopropionase / GpuA | ||||||
Function / homology | Function and homology information guanidinopropionase / guanidinopropionase activity / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.07 Å | ||||||
Authors | Lee, S.J. / Kim, H.S. / Kim, D.J. / Yoon, H.J. / Kim, K.H. / Yoon, J.Y. / Jang, J.Y. / Im, H. / An, D. / Suh, S.W. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Crystal structures of Pseudomonas aeruginosa guanidinobutyrase and guanidinopropionase, members of the ureohydrolase superfamily Authors: Lee, S.J. / Kim, D.J. / Kim, H.S. / Lee, B.I. / Yoon, H.J. / Yoon, J.Y. / Kim, K.H. / Jang, J.Y. / Im, H.N. / An, D.R. / Song, J.S. / Kim, H.J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3niq.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3niq.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 3niq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3niq_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 3niq_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 3niq_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 3niq_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/3niq ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3niq | HTTPS FTP |
-Related structure data
Related structure data | 3nioSC 3nipC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35297.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: gpuA, PA0288 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q9I6K2, guanidinopropionase #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-MN / #4: 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: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES at pH 6.5, 12% (w/v) PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→20 Å / Num. obs: 38934 / % possible obs: 100 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 30.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 3NIO Resolution: 2.07→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.11 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.176 / 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: 28.955 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.069→2.123 Å / Total num. of bins used: 20
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