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- PDB-5kdp: E491A mutant of choline TMA-lyase -

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Basic information

Entry
Database: PDB / ID: 5kdp
TitleE491A 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 / 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. / 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
MALONATE ION / Choline trimethylamine-lyase
Similarity search - Component
Biological speciesDesulfovibrio alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFunk, M.A. / Drennan, C.L.
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
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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
C: Choline trimethylamine-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,71410
Polymers183,0562
Non-polymers6588
Water28,5721586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-16 kcal/mol
Surface area50630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.922, 228.922, 78.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 91528.086 Da / Num. of mol.: 2 / Mutation: E491A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio alaskensis (bacteria) / Strain: G20 / Gene: cutC, 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.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1586 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.45 % / Description: large, thin rods
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.0-1.2 M sodium malonate pH 7.0-8.0 / PH range: 7-8 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 164734 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 26.35 Å2 / Rsym value: 0.1 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 4.06 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAW

5faw


Resolution: 1.9→49.471 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 4917 3 %random
Rwork0.2144 ---
obs0.2153 163752 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12666 0 44 1588 14298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313027
X-RAY DIFFRACTIONf_angle_d0.61617644
X-RAY DIFFRACTIONf_dihedral_angle_d16.3217828
X-RAY DIFFRACTIONf_chiral_restr0.0391892
X-RAY DIFFRACTIONf_plane_restr0.0042305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9216-1.94420.32334100.30034924X-RAY DIFFRACTION100
1.9679-1.99280.31354100.28664969X-RAY DIFFRACTION100
2.0467-2.0760.29714090.27344994X-RAY DIFFRACTION100
2.1069-2.13990.28254100.26195032X-RAY DIFFRACTION100
2.2125-2.25270.28794100.25525040X-RAY DIFFRACTION100
2.296-2.34290.28584100.2485022X-RAY DIFFRACTION100
2.4495-2.51080.25534080.23835028X-RAY DIFFRACTION100
2.5786-2.65450.27734100.24435038X-RAY DIFFRACTION100
2.8381-2.95170.26594100.22545062X-RAY DIFFRACTION100
3.0861-3.24870.23744100.2185049X-RAY DIFFRACTION100
3.7187-4.09280.19854100.17375136X-RAY DIFFRACTION100
4.6846-5.90060.18574100.15145188X-RAY DIFFRACTION99
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)
10.3780.26460.03910.3496-0.15780.20470.0372-0.06450.05650.18340.03260.1013-0.1551-0.50390.0660.15030.05790.02390.58410.00830.3086453.9197-38.043544.3748
20.3030.0226-0.1340.25460.1640.2338-0.00820.08030.1359-0.17410.09280.1411-0.3852-0.49370.0610.15860.2143-0.00220.47450.05660.2984460.5242-25.566832.1643
3-0.00070.0515-0.04460.1513-0.1770.2020.0523-0.07190.0160.123-0.0027-0.0266-0.0089-0.28360.01050.1341-0.0070.01730.3475-0.0050.2073463.4353-42.897850.8934
40.15590.0634-0.1730.2265-0.13170.3563-0.04070.04160.0237-0.09620.07120.01070.1902-0.4610.03370.1454-0.097-0.00380.44260.02450.2313460.8715-54.261932.5497
50.11-0.0230.1020.00790.00370.08790.0084-0.01230.0367-0.0186-0.0201-0.0194-0.1053-0.010600.1732-0.0045-0.00990.23620.01270.2028477.5805-32.7289.798
60.0943-0.0077-0.19150.14780.04620.39290.0280.0402-0.0056-0.05170.00330.00370.0581-0.3884-0.00160.1569-0.0226-0.0260.3160.01030.2285469.0618-44.609410.9975
70.21410.03730.0410.0491-0.09250.33590.04230.07580.02120.07840.04970.1298-0.0857-0.68790.02050.2036-0.059-0.01710.69490.03190.2874450.9124-50.510715.8143
80.0166-0.0267-0.06850.17560.29030.4468-0.11890.0813-0.0839-0.13260.0402-0.06080.22590.3911-0.18280.43470.1290.03670.1663-0.02630.2002514.1772-74.074411.2886
90.16230.0166-0.16280.15090.07530.24880.0493-0.1596-0.11960.0088-0.1173-0.01040.45680.4395-0.03830.46690.22810.0040.22070.02860.2106515.4822-78.785530.1751
100.0936-0.0059-0.07170.12870.02010.18090.00680.11730.0111-0.0161-0.0214-0.02010.09570.14250.00010.23280.04560.00560.2120.01030.204513.4535-57.859316.3293
110.41980.01180.16680.12880.13020.47760.02040.0493-0.0203-0.0375-0.00870.02760.3033-0.04930.00050.30850.0080.01080.142-0.00860.1937497.1491-71.589810.4274
120.10550.10260.02360.0968-0.01410.33140.149-0.16450.02830.1722-0.11470.04030.24740.0880.01290.3871-0.04270.04310.18260.02020.1677492.475-76.917448.3156
130.22850.01790.14940.27120.10910.16230.07660.0575-0.10330.0602-0.0869-0.00130.4452-0.0241-0.00920.5054-0.12310.01020.0853-0.03070.2022487.6941-79.397738.2704
140.26380.12340.10990.31580.15650.2479-0.0043-0.151-0.06910.0592-0.03180.08370.5762-0.20560.01940.6079-0.11890.0280.0889-0.00880.2513486.5397-84.614226.6078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 330 )
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 505 )
5X-RAY DIFFRACTION5chain 'A' and (resid 506 through 574 )
6X-RAY DIFFRACTION6chain 'A' and (resid 575 through 770 )
7X-RAY DIFFRACTION7chain 'A' and (resid 771 through 846 )
8X-RAY DIFFRACTION8chain 'C' and (resid 41 through 110 )
9X-RAY DIFFRACTION9chain 'C' and (resid 111 through 207 )
10X-RAY DIFFRACTION10chain 'C' and (resid 208 through 285 )
11X-RAY DIFFRACTION11chain 'C' and (resid 286 through 504 )
12X-RAY DIFFRACTION12chain 'C' and (resid 505 through 574 )
13X-RAY DIFFRACTION13chain 'C' and (resid 575 through 665 )
14X-RAY DIFFRACTION14chain 'C' and (resid 666 through 846 )

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