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Yorodumi- PDB-2vhh: Crystal structure of a pyrimidine degrading enzyme from Drosophil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vhh | ||||||
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Title | Crystal structure of a pyrimidine degrading enzyme from Drosophila melanogaster | ||||||
Components | CG3027-PA | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Pyrimidine catabolism / beta-ureidopropionase / pyrimidine nucleobase catabolic process / N-carbamoylputrescine amidase activity / beta-alanine biosynthetic process via 3-ureidopropionate / putrescine biosynthetic process from arginine / beta-ureidopropionase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lundgren, S. / Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The Crystal Structure of Beta-Alanine Synthase from Drosophila Melanogaster Reveals a Homooctameric Helical Turn-Like Assembly. Authors: Lundgren, S. / Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vhh.cif.gz | 286.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vhh.ent.gz | 235.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vhh_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 2vhh_full_validation.pdf.gz | 485.9 KB | Display | |
Data in XML | 2vhh_validation.xml.gz | 50.2 KB | Display | |
Data in CIF | 2vhh_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/2vhh ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vhh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 2
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 46124.949 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VI04, beta-ureidopropionase |
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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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 4.2 / Details: PEG 3350,PHOSPHATE/CITRATE PH 4.2, NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. obs: 43922 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 94.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.877 / SU B: 14.178 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→35 Å
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Refine LS restraints |
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