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- PDB-9f3y: CutC choline lyase in complex with difluorocholine -

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Basic information

Entry
Database: PDB / ID: 9f3y
TitleCutC choline lyase in complex with difluorocholine
ComponentsCholine trimethylamine-lyase
KeywordsLYASE / glycyl radical enzyme / choline / CutC
Function / homology
Function and homology information


choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process
Similarity search - Function
Choline trimethylamine-lyase / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
: / Choline trimethylamine-lyase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKalnins, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionApr 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Choline trimethylamine-lyase
B: Choline trimethylamine-lyase
C: Choline trimethylamine-lyase
D: Choline trimethylamine-lyase
E: Choline trimethylamine-lyase
F: Choline trimethylamine-lyase
G: Choline trimethylamine-lyase
H: Choline trimethylamine-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,027,77516
Polymers1,026,7828
Non-polymers9938
Water3,981221
1
A: Choline trimethylamine-lyase
hetero molecules

D: Choline trimethylamine-lyase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 257 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)256,9444
Polymers256,6962
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2590 Å2
ΔGint-9 kcal/mol
Surface area48160 Å2
MethodPISA
2
B: Choline trimethylamine-lyase
hetero molecules

E: Choline trimethylamine-lyase
hetero molecules


  • defined by author&software
  • 257 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)256,9444
Polymers256,6962
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2750 Å2
ΔGint-6 kcal/mol
Surface area47840 Å2
MethodPISA
3
C: Choline trimethylamine-lyase
G: Choline trimethylamine-lyase
hetero molecules


  • defined by author&software
  • 257 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)256,9444
Polymers256,6962
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-9 kcal/mol
Surface area48310 Å2
MethodPISA
4
F: Choline trimethylamine-lyase
H: Choline trimethylamine-lyase
hetero molecules


  • defined by author&software
  • 257 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)256,9444
Polymers256,6962
Non-polymers2482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-9 kcal/mol
Surface area47820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.366, 117.573, 212.531
Angle α, β, γ (deg.)77.650, 85.337, 70.007
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Choline trimethylamine-lyase / Choline TMA-lyase / Choline utilization protein C


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 / difluorocholine / 2-DEOXY-2-FLUOROHEXOPYRANOSYL FLUORIDE / 2-DEOXY-2-FLUORO-ALPHA-D-MANNOSYL FLUORIDE / 2-deoxy-2-fluoro-beta-D-mannosyl fluoride / 2-deoxy-2-fluoro-D-mannosyl fluoride / 2-deoxy-2-fluoro-mannosyl fluoride


Mass: 124.152 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12F2N / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 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

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2947 8184 4.9 %
Rwork0.22 158740 -
obs0.2236 166924 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50032 0 64 221 50317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010151136
X-RAY DIFFRACTIONf_angle_d1.255169192
X-RAY DIFFRACTIONf_chiral_restr0.05927560
X-RAY DIFFRACTIONf_plane_restr0.00719024
X-RAY DIFFRACTIONf_dihedral_angle_d8.20236984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.930.36942870.30325462X-RAY DIFFRACTION97.79
2.93-2.970.34952820.29755340X-RAY DIFFRACTION97.71
2.97-30.36462840.29975351X-RAY DIFFRACTION97.59
3-3.040.35692710.29355409X-RAY DIFFRACTION97.48
3.04-3.080.38132990.30145350X-RAY DIFFRACTION96.96
3.08-3.120.36823050.29275294X-RAY DIFFRACTION96.97
3.12-3.170.37712950.27855358X-RAY DIFFRACTION97.15
3.17-3.220.33272810.2695244X-RAY DIFFRACTION96.68
3.22-3.270.33512850.25455476X-RAY DIFFRACTION96.95
3.27-3.320.3462390.25215229X-RAY DIFFRACTION95.91
3.32-3.380.34332800.26215280X-RAY DIFFRACTION95.08
3.38-3.440.33372570.26215233X-RAY DIFFRACTION94.57
3.44-3.50.32322370.25234952X-RAY DIFFRACTION90.2
3.5-3.580.29662800.22985151X-RAY DIFFRACTION93.62
3.58-3.650.32482700.24215423X-RAY DIFFRACTION97.6
3.65-3.740.29832950.22385319X-RAY DIFFRACTION97.33
3.74-3.830.29842910.21235361X-RAY DIFFRACTION97.11
3.83-3.940.29942780.21875314X-RAY DIFFRACTION96.6
3.94-4.050.26192810.21295390X-RAY DIFFRACTION97.17
4.05-4.180.27272550.19815365X-RAY DIFFRACTION96.83
4.18-4.330.26242800.19425213X-RAY DIFFRACTION95.71
4.33-4.50.2442840.19315204X-RAY DIFFRACTION94.31
4.5-4.710.27122770.19325021X-RAY DIFFRACTION90.81
4.71-4.960.27272640.18855372X-RAY DIFFRACTION97.75
4.96-5.270.26212640.19435384X-RAY DIFFRACTION97.28
5.27-5.670.28252640.19195353X-RAY DIFFRACTION96.95
5.67-6.240.27722480.20235305X-RAY DIFFRACTION95.3
6.24-7.140.29122530.20395027X-RAY DIFFRACTION91.51
7.14-8.990.25052510.17185379X-RAY DIFFRACTION96.84
8.99-44.570.22522470.16585181X-RAY DIFFRACTION93.49

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