+Open data
-Basic information
Entry | Database: PDB / ID: 3nio | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa guanidinobutyrase | ||||||
Components | Guanidinobutyrase | ||||||
Keywords | HYDROLASE / PA1421 / guanidinobutyrase / GbuA | ||||||
Function / homology | Function and homology information guanidinobutyrase / guanidinobutyrase activity / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / arginine catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 3nio.cif.gz | 379.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nio.ent.gz | 310.9 KB | Display | PDB format |
PDBx/mmJSON format | 3nio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nio_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
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Full document | 3nio_full_validation.pdf.gz | 481 KB | Display | |
Data in XML | 3nio_validation.xml.gz | 76.1 KB | Display | |
Data in CIF | 3nio_validation.cif.gz | 105.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/3nio ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3nio | HTTPS FTP |
-Related structure data
Related structure data | 3nipC 3niqC 1gq7S 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: 34956.043 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: gbuA, PA1421 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9I3S3, guanidinobutyrase #2: Chemical | ChemComp-MN / #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: 2.39 Å3/Da / Density % sol: 48.44 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10mM cobalt(II) chloride, 0.1M MES at pH 6.5, 1.8M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.0626 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0626 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 133054 / % possible obs: 99.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 24.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GQ7 Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.586 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R Free: 0.18 / 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: 22.647 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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