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Yorodumi- PDB-4lao: Crystal structure of Cordyceps militaris IDCase H195A mutant (Zn) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lao | ||||||
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Title | Crystal structure of Cordyceps militaris IDCase H195A mutant (Zn) | ||||||
Components | Cordyceps militaris IDCase | ||||||
Keywords | LYASE / pyrimidine metabolism / IDCase / decarboxylase / uracil / DNA decarboxylation | ||||||
Function / homology | Function and homology information organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Cordyceps militaris (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Xu, S. / Li, W. / 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 | 4lao.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lao.ent.gz | 247.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4lao ftp://data.pdbj.org/pub/pdb/validation_reports/la/4lao | HTTPS FTP |
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-Related structure data
Related structure data | 4hjwC 4hk5SC 4hk6C 4hk7C 4lakC 4lalC 4lamC 4lanC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40653.883 Da / Num. of mol.: 2 / Mutation: H195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cordyceps militaris (fungus) / Strain: CM01 / Gene: CCM_01452 / Plasmid: pET28Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: G3J531 #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: 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: 2.6 Å3/Da / Density % sol: 52.68 % / Mosaicity: 0.596 ° |
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Crystal grow | Temperature: 289 K / Method: sitting drop / pH: 5.6 Details: 30% polyethylene glycol 4000, 0.2M NH4Ac, 2mM ZnCl2, 0.1M sodium citrate, pH 5.6, sitting drop, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 55498 / % possible obs: 97.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.062 / Χ2: 1.042 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HK5 Resolution: 2→45.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.809 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 157.27 Å2 / Biso mean: 38.0096 Å2 / Biso min: 15.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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