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- PDB-6vue: wild-type choline TMA lyase in complex with 1-methyl-1,2,3,6-tetr... -

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Basic information

Entry
Database: PDB / ID: 6vue
Titlewild-type choline TMA lyase in complex with 1-methyl-1,2,3,6-tetrahydropyridin-3-ol
ComponentsCholine trimethylamine-lyase
KeywordsLYASE/INHIBITOR / Choline-TMA Lyase / Microbiome choline CutC inhibitor / LYASE / LYASE-INHIBITOR complex
Function / homology
Function and homology information


choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process / choline binding / protein homodimerization activity / cytosol
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
(3S)-1-methyl-1,2,3,6-tetrahydropyridin-3-ol / Choline trimethylamine-lyase
Similarity search - Component
Biological speciesDesulfovibrio alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsOrtega, M.A. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
Other private United States
Other private United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria.
Authors: Bollenbach, M. / Ortega, M. / Orman, M. / Drennan, C.L. / Balskus, E.P.
History
DepositionFeb 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,4456
Polymers183,1722
Non-polymers2724
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-26 kcal/mol
Surface area49400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.525, 228.525, 78.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1085-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 53 through 241 or (resid 242...
21(chain B and (resid 53 through 66 or (resid 67...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEU(chain A and (resid 53 through 241 or (resid 242...AA53 - 24122 - 210
12GLUGLUGLUGLU(chain A and (resid 53 through 241 or (resid 242...AA242211
13GLYGLYPHEPHE(chain A and (resid 53 through 241 or (resid 242...AA44 - 84613 - 815
14GLYGLYPHEPHE(chain A and (resid 53 through 241 or (resid 242...AA44 - 84613 - 815
15GLYGLYPHEPHE(chain A and (resid 53 through 241 or (resid 242...AA44 - 84613 - 815
16GLYGLYPHEPHE(chain A and (resid 53 through 241 or (resid 242...AA44 - 84613 - 815
21GLYGLYLYSLYS(chain B and (resid 53 through 66 or (resid 67...BB53 - 6622 - 35
22GLUGLUGLUGLU(chain B and (resid 53 through 66 or (resid 67...BB6736
23VALVALPHEPHE(chain B and (resid 53 through 66 or (resid 67...BB46 - 84615 - 815
24VALVALPHEPHE(chain B and (resid 53 through 66 or (resid 67...BB46 - 84615 - 815
25VALVALPHEPHE(chain B and (resid 53 through 66 or (resid 67...BB46 - 84615 - 815
26VALVALPHEPHE(chain B and (resid 53 through 66 or (resid 67...BB46 - 84615 - 815

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Components

#1: Protein Choline trimethylamine-lyase / Choline TMA-lyase / Choline utilization protein C / Glycyl radical enzyme CutC / GRE CutC


Mass: 91586.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio alaskensis (strain G20) (bacteria)
Strain: G20 / Gene: cutC, Dde_3282 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q30W70, choline trimethylamine-lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-RP7 / (3S)-1-methyl-1,2,3,6-tetrahydropyridin-3-ol


Mass: 113.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 1.3 M sodium malonate pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.276→50 Å / Num. obs: 94805 / % possible obs: 99.4 % / Redundancy: 21.8 % / Biso Wilson estimate: 24.68 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.036 / Rrim(I) all: 0.177 / Χ2: 1.043 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.367.80.57188450.7970.1940.6080.98294.4
2.36-2.4612.40.61794000.870.1740.6431.02299.6
2.46-2.5718.70.60194340.9390.1410.6181.049100
2.57-2.722.60.52793960.9610.1130.5391.087100
2.7-2.8724.80.41294640.9790.0840.4211.106100
2.87-3.0927.20.29694910.990.0580.3011.132100
3.09-3.4126.70.19395190.9950.0380.1971.075100
3.41-3.925.10.12395590.9980.0250.1250.998100
3.9-4.9126.20.08396570.9990.0160.0840.977100
4.91-5025.60.065100400.9990.0130.0670.958100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau


Resolution: 2.28→49.386 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.1973 4637 4.98 %
Rwork0.1637 --
obs0.1654 93182 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.9 Å2 / Biso mean: 25.0086 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 2.28→49.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12573 0 40 476 13089
Biso mean--24.39 23.81 -
Num. residues----1604
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7687X-RAY DIFFRACTION5.658TORSIONAL
12B7687X-RAY DIFFRACTION5.658TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.30140.24161250.2039238380
2.3014-2.32850.23431480.2094281294
2.3285-2.35690.26111520.2017289097
2.3569-2.38670.24791570.1997297399
2.3867-2.41810.23351560.20092969100
2.4181-2.45120.23641580.19393000100
2.4512-2.48630.25281580.18952985100
2.4863-2.52340.24041570.19082999100
2.5234-2.56280.27141580.19752981100
2.5628-2.60480.2421570.19383001100
2.6048-2.64970.23961580.19182999100
2.6497-2.69790.24221580.19623005100
2.6979-2.74980.25521580.20033003100
2.7498-2.80590.24921590.20713032100
2.8059-2.86690.23861570.2142971100
2.8669-2.93360.23441590.20863022100
2.9336-3.0070.26491580.20993012100
3.007-3.08830.20891590.20113005100
3.0883-3.17910.23561600.18673044100
3.1791-3.28170.18831590.17633023100
3.2817-3.3990.2121600.16333021100
3.399-3.5350.1971570.14963018100
3.535-3.69590.15241610.13553046100
3.6959-3.89060.15041600.12833040100
3.8906-4.13430.14771620.11963069100
4.1343-4.45330.14841610.11853051100
4.4533-4.90110.14031620.1184305399
4.9011-5.60940.16271510.1329293995
5.6094-7.0640.17351210.148261683
7.064-49.3860.13871310.1271258378

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