+Open data
-Basic information
Entry | Database: PDB / ID: 4y0w | ||||||
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Title | YeaZ from Pseudomonas aeruginosa | ||||||
Components | YeaZ | ||||||
Keywords | BIOSYNTHETIC PROTEIN / essential protein involved in the biosynthesis of threonylcarbamoyl adenosine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO579 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Milani, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Crystal structure of YeaZ from Pseudomonas aeruginosa. Authors: Vecchietti, D. / Ferrara, S. / Rusmini, R. / Macchi, R. / Milani, M. / Bertoni, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y0w.cif.gz | 206.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y0w.ent.gz | 171.6 KB | Display | PDB format |
PDBx/mmJSON format | 4y0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/4y0w ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y0w | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25032.518 Da / Num. of mol.: 5 / Fragment: residues 7-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO579 (bacteria) Gene: A161_18155 / Production host: Escherichia coli (E. coli) / References: UniProt: K0Y2M1, UniProt: A0A140UHA7*PLUS #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 4M Sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.22 Å / Num. obs: 43728 / % possible obs: 99.9 % / Redundancy: 5.9 % / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.281 / 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: 76.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→43.22 Å
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Refine LS restraints |
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