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Yorodumi- PDB-5a0u: Structure of CutC choline lyase choline bound form from Klebsiell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a0u | ||||||
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Title | Structure of CutC choline lyase choline bound form from Klebsiella pneumoniae. | ||||||
Components | CHOLINE TRIMETHYLAMINE LYASE | ||||||
Keywords | LYASE / CUTC / CHOLINE TMA LYASE / GLYCYL RADICAL ENZYME | ||||||
Function / homology | Function and homology information choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process Similarity search - Function | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kalnins, G. / Tars, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structure and Function of Cutc Choline Lyase from Human Microbiota Bacterium Klebsiella Pneumoniaee Authors: Kalnins, G. / Kuka, J. / Grinberga, S. / Makrecka-Kuka, M. / Liepinsh, E. / Dambrova, M. / Tars, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a0u.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5a0u.ent.gz | 1023.6 KB | Display | PDB format |
PDBx/mmJSON format | 5a0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0u ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0u | HTTPS FTP |
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-Related structure data
Related structure data | 5a0zC 1r9dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 89476.922 Da / Num. of mol.: 8 / Fragment: RESIDUES 334-1028 Source method: isolated from a genetically manipulated source Details: N_TERMINUS CLEAVED WITH CHYMOTRYPSN LEAVING VARIABLE N-TERMINAL SEQUENCE Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Description: THE MICROBIAL STRAIN COLLECTION OF LATVIA / Plasmid: PRSF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL44*PLUS #2: Chemical | ChemComp-CHT / #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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 20% PEG 3350, 60-20 MM K/NA TARTRATE, 100 MM BIS-TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 |
Detector | Type: RAYONIX / Detector: CCD / Date: Dec 12, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→209.74 Å / Num. obs: 289262 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.8 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R9D Resolution: 2.4→209.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.181 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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 mean: 28.181 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→209.74 Å
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Refine LS restraints |
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