+Open data
-Basic information
Entry | Database: PDB / ID: 9f3y | ||||||
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Title | CutC choline lyase in complex with difluorocholine | ||||||
Components | Choline trimethylamine-lyase | ||||||
Keywords | LYASE / glycyl radical enzyme / choline / CutC | ||||||
Function / homology | Function and homology information choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kalnins, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: CutC choline lyase in complex with difluorocholine Authors: Kalnins, G. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f3y.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9f3y.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9f3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f3y_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 9f3y_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 9f3y_validation.xml.gz | 238.6 KB | Display | |
Data in CIF | 9f3y_validation.cif.gz | 319.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/9f3y ftp://data.pdbj.org/pub/pdb/validation_reports/f3/9f3y | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 128347.758 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: hpdB, cutC, SAMEA4873561_02933, SAMEA4873648_04511 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A486V7R5, choline trimethylamine-lyase #2: Chemical | ChemComp-A1H9L / Mass: 124.152 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12F2N / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 61 mM K/Na tartrate, 18% PEG3350, 12.5 mM EDTA, 100 mM Bis-Tris (pH 7.5) |
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-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.73 Å / Num. obs: 167016 / % possible obs: 95.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.18 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.16 / Rrim(I) all: 0.227 / Χ2: 0.94 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8505 / CC1/2: 0.591 / Rpim(I) all: 0.84 / Rrim(I) all: 1.188 / Χ2: 0.83 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.57 Å / SU ML: 0.472 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.3778 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→44.57 Å
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Refine LS restraints |
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LS refinement shell |
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