+Open data
-Basic information
Entry | Database: PDB / ID: 9f3x | ||||||
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Title | CutC choline lyase in complex with cyclopropylcholine | ||||||
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: 2.7 Å | ||||||
Authors | Kalnins, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: CutC choline lyase in complex with fluoromethylcholine 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 | 9f3x.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9f3x.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9f3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f3x_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 9f3x_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 9f3x_validation.xml.gz | 225.8 KB | Display | |
Data in CIF | 9f3x_validation.cif.gz | 304.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/9f3x ftp://data.pdbj.org/pub/pdb/validation_reports/f3/9f3x | HTTPS FTP |
-Related structure data
Related structure data | 9f3wC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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-A1H9K / Mass: 130.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H16NO / 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 | Density % sol: 39.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 80 mM K/Na tartrate, 18% PEG3350, 10 mM EDTA, 100 mM Bis-Tris (pH 7.5) |
-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: 2.7→49.41 Å / Num. obs: 213547 / % possible obs: 95.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.9 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.184 / Rrim(I) all: 0.26 / Χ2: 0.94 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 1.211 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10553 / CC1/2: 0.361 / Rpim(I) all: 1.211 / Rrim(I) all: 1.712 / Χ2: 0.92 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.64 Å / SU ML: 0.4261 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.3373 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: 44.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.64 Å
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Refine LS restraints |
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LS refinement shell |
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