+Open data
-Basic information
Entry | Database: PDB / ID: 4hk5 | ||||||
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Title | Crystal structure of Cordyceps militaris IDCase in apo form | ||||||
Components | Uracil-5-carboxylate decarboxylase | ||||||
Keywords | LYASE / pyrimidine metabolism / DNA decarboxylation / IDCase / decarboxylase / uracil | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cordyceps militaris (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Xu, S. / Zhu, J. / Ding, J. | ||||||
Citation | Journal: Cell Res. / Year: 2013 Title: Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase. Authors: Xu, S. / Li, W. / Zhu, J. / Wang, R. / Li, Z. / Xu, G.L. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hk5.cif.gz | 588.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hk5.ent.gz | 485.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hk5_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 4hk5_full_validation.pdf.gz | 474.4 KB | Display | |
Data in XML | 4hk5_validation.xml.gz | 58 KB | Display | |
Data in CIF | 4hk5_validation.cif.gz | 85.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/4hk5 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/4hk5 | HTTPS FTP |
-Related structure data
Related structure data | 4hjwC 4hk6C 4hk7C 4lakC 4lalC 4lamC 4lanC 4laoC 2wm1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42067.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cordyceps militaris (fungus) / Gene: CCM_01452 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: G3J531, EC: 4.1.1.66 #2: Chemical | ChemComp-ZN / #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: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→77.266 Å / Num. obs: 135002 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Χ2: 1.022 / Net I/σ(I): 9.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WM1 Resolution: 1.9→77.266 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 92.3 Å2 / Biso mean: 21.9296 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→77.266 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.946 Å / Total num. of bins used: 20
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