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Yorodumi- PDB-3nip: Crystal structure of Pseudomonas aeruginosa guanidinopropionase c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nip | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa guanidinopropionase complexed with 1,6-diaminohexane | ||||||
Components | 3-guanidinopropionase | ||||||
Keywords | HYDROLASE / guanidinopropionase / GpuA / PA0288 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 3nip.cif.gz | 356.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nip.ent.gz | 291.9 KB | Display | PDB format |
PDBx/mmJSON format | 3nip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/3nip ftp://data.pdbj.org/pub/pdb/validation_reports/ni/3nip | HTTPS FTP |
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-Related structure data
Related structure data | 3nioSC 3niqC 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
#1: Protein | Mass: 35297.945 Da / Num. of mol.: 6 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-16D / #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: 3.58 Å3/Da / Density % sol: 65.64 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M lithium sulfate, 0.1M tri-sodium citrate at pH 5.6, 12% (w/v) PEG 6000, 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: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 101621 / % possible obs: 99.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NIO Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.928 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.227 / 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: 26.193 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.501→2.565 Å / Total num. of bins used: 20
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