+Open data
-Basic information
Entry | Database: PDB / ID: 2h0j | ||||||
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Title | Crystal structure of PucM in the presence of 5,6-diaminouracil | ||||||
Components | Transthyretin-like protein pucM | ||||||
Keywords | HYDROLASE / BETA SANDWITCH / COMPLEX WITH DIAMINOURACIL / HIU | ||||||
Function / homology | Function and homology information hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / urate catabolic process / purine nucleobase metabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å | ||||||
Authors | Rhee, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural and functional analysis of PucM, a hydrolase in the ureide pathway and a member of the transthyretin-related protein family. Authors: Jung, D.-K. / Lee, Y. / Park, S.G. / Park, B.C. / Kim, G.-H. / Rhee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h0j.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h0j.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 2h0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/2h0j ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h0j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Chain A and B forms independently a homotetramer by a crystallographic symmetry-related molecules |
-Components
#1: Protein | Mass: 13703.716 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32142 #2: Chemical | ChemComp-URN / | #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: 3.52 Å3/Da / Density % sol: 65.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.2 Details: 0.1M ammonium acetate, 0.5M NaCl, 0.5M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97144 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 16, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97144 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→30 Å / Num. all: 9261 / Num. obs: 9261 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.107 / Χ2: 0.823 / Net I/σ(I): 7.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→30 Å / σ(F): 991 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 20.282 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Xplor file |
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