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- PDB-5fay: Y208F mutant of choline TMA-lyase -

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Basic information

Entry
Database: PDB / ID: 5fay
TitleY208F mutant of choline TMA-lyase
ComponentsCholine trimethylamine-lyase
KeywordsLYASE / mutant / radical
Function / homology
Function and homology information


choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process / choline binding / protein homodimerization activity
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. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain ...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. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / MALONATE ION / Choline trimethylamine-lyase
Similarity search - Component
Biological speciesDesulfovibrio alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsFunk, M.A. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)0645960 United States
CitationJournal: Cell Chem Biol / Year: 2016
Title: Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase.
Authors: Bodea, S. / Funk, M.A. / Balskus, E.P. / Drennan, C.L.
History
DepositionDec 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)184,33616
Polymers183,1402
Non-polymers1,19614
Water42,6782369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-2 kcal/mol
Surface area49930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.941, 228.941, 78.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-179-

LYS

21A-1189-

HOH

31A-1691-

HOH

41A-2123-

HOH

51A-2236-

HOH

61B-1894-

HOH

71B-1937-

HOH

81B-1955-

HOH

DetailsSize exclusion chromatography

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Components

#1: Protein Choline trimethylamine-lyase


Mass: 91570.125 Da / Num. of mol.: 2 / Mutation: Y208F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio alaskensis (bacteria) / Strain: G20 / Gene: Dde_3282 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q30W70, choline trimethylamine-lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2369 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.45 % / Description: Crystals were rod-like and grew within 7 days.
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: Protein at 8 mg/mL in buffer containing 50 mM potassium phosphate pH 8.0, 50 mM potassium chloride, and 10 mM choline was mixed in a 1:1 ratio with well solution containing 1.0-1.2 M sodium malonate pH 7.0-8.0.
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 163497 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rsym value: 0.124 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau


Resolution: 1.901→49.48 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 4901 3 %
Rwork0.1589 --
obs0.16 163402 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12483 0 80 2369 14932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613122
X-RAY DIFFRACTIONf_angle_d0.92517770
X-RAY DIFFRACTIONf_dihedral_angle_d13.244881
X-RAY DIFFRACTIONf_chiral_restr0.0341897
X-RAY DIFFRACTIONf_plane_restr0.0042327
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8968-0.44730.34070.9476-0.68161.2796-0.0899-0.2036-0.03180.13120.03790.00460.1797-0.2490.03360.3474-0.09610.04060.1719-0.01110.2045-56.161-74.064528.1611
20.31770.03540.13230.4199-0.06020.883-0.01070.038-0.0884-0.0640.00530.04970.4772-0.38090.0120.3728-0.13440.01610.2061-0.01890.2312-57.4479-78.77789.2795
30.227-0.26110.20840.3484-0.38861.6385-0.0642-0.04790.00560.09810.02680.01390.0854-0.27130.04730.1727-0.05490.01530.177-0.02590.2064-55.5661-57.848223.1113
40.71040.0731-0.05920.5703-0.07790.72920.0119-0.0682-0.0690.0743-0.0293-0.02720.2592-0.01180.01820.2719-0.02310.01570.12340.00640.2024-39.1833-71.650228.8701
51.0951-0.7888-0.47011.45130.61251.30640.07130.163-0.0727-0.1725-0.0821-0.1030.24260.02270.01530.2776-0.01060.02860.14050.00690.209-35.5402-73.223-2.0361
61.029-0.80770.09061.5327-0.00740.56640.08170.175-0.1291-0.3003-0.0941-0.14470.39970.12750.01280.45360.05780.05910.2241-0.01220.2803-25.2975-83.0436-2.317
70.78350.0595-0.22110.73910.00140.67030.025-0.0307-0.15260.0197-0.0871-0.0950.53820.18180.02870.54130.04010.04140.11130.0190.3035-28.0167-88.245216.5236
80.5708-0.2461-0.02680.3660.02860.7477-0.0203-0.01780.06080.00310.008-0.0986-0.10020.4096-0.0230.1356-0.03280.0190.3622-0.010.22374.3382-34.6233-1.1504
91.5410.1614-0.16131.1818-0.17440.96650.04480.01970.10160.03190.0231-0.1084-0.35440.2767-0.05680.2044-0.0626-0.00190.209-0.0330.1905-10.0426-20.999210.7848
101.1121-0.7958-0.31290.79670.29040.7530.10860.1657-0.0171-0.0908-0.06180.0173-0.00710.1802-0.05840.135-0.01420.00540.18470.00520.1429-11.3689-39.6808-11.6665
110.57460.0348-0.13810.4299-0.06751.0466-0.0183-0.018-0.06130.00120.0179-0.07540.14610.31170.00750.14570.05870.00450.2705-0.00460.1909-1.2429-52.87983.2213
120.3903-0.04220.34440.1444-0.0992.6631-0.0158-0.07120.01450.0624-0.00860.0224-0.0669-0.01280.02750.13010.00610.00710.1584-0.00190.1722-18.3496-36.675423.462
130.4676-0.17520.45340.4127-0.13622.41510.0032-0.0696-0.00730.07240.0171-0.0008-0.00280.2005-0.02290.15620.01160.01190.21780.00060.1995-13.01-42.153435.443
140.7422-0.2005-0.20641.6080.1950.80630.0018-0.0994-0.08310.08350.0249-0.19360.18490.3192-0.03410.1860.0606-0.01930.30660.02260.1933-3.1052-53.843729.0796
151.43330.8382-0.25891.863-0.09631.11710.0414-0.0686-0.00410.0926-0.0202-0.2691-0.03670.5404-0.03060.19650.0432-0.00280.511-0.01110.24928.9034-46.291723.4186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 67:110 )B67 - 110
2X-RAY DIFFRACTION2( CHAIN B AND RESID 111:207 )B111 - 207
3X-RAY DIFFRACTION3( CHAIN B AND RESID 208:285 )B208 - 285
4X-RAY DIFFRACTION4( CHAIN B AND RESID 286:505 )B286 - 505
5X-RAY DIFFRACTION5( CHAIN B AND RESID 506:626 )B506 - 626
6X-RAY DIFFRACTION6( CHAIN B AND RESID 627:709 )B627 - 709
7X-RAY DIFFRACTION7( CHAIN B AND RESID 710:846 )B710 - 846
8X-RAY DIFFRACTION8( CHAIN A AND RESID 44:161 )A44 - 161
9X-RAY DIFFRACTION9( CHAIN A AND RESID 162:207 )A162 - 207
10X-RAY DIFFRACTION10( CHAIN A AND RESID 208:285 )A208 - 285
11X-RAY DIFFRACTION11( CHAIN A AND RESID 286:505 )A286 - 505
12X-RAY DIFFRACTION12( CHAIN A AND RESID 506:626 )A506 - 626
13X-RAY DIFFRACTION13( CHAIN A AND RESID 627:709 )A627 - 709
14X-RAY DIFFRACTION14( CHAIN A AND RESID 710:787 )A710 - 787
15X-RAY DIFFRACTION15( CHAIN A AND RESID 788:846 )A788 - 846

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