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- PDB-5a0z: STRUCTURE OF CUTC CHOLINE LYASE CHOLINE FREE FORM FROM KLEBSIELLA... -

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Basic information

Entry
Database: PDB / ID: 5a0z
TitleSTRUCTURE OF CUTC CHOLINE LYASE CHOLINE FREE FORM FROM KLEBSIELLA PNEUMONIAE
ComponentsCHOLINE TRIMETHYLAMINE LYASE
KeywordsLYASE / CUTC / CHOLINE TMA LYASE / GLYCYL RADICAL ENZYME
Function / homology
Function and homology information


choline trimethylamine-lyase / choline trimethylamine lyase activity / choline catabolic process / 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. ...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 trimethylamine-lyase
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKalnins, G. / Tars, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure and Function of Cutc Choline Lyase from Human Microbiota Bacterium Klebsiella Pneumoniaee
Authors: Kalnins, G. / Kuka, J. / Grinberga, S. / Makrecka-Kuka, M. / Liepinsh, E. / Dambrova, M. / Tars, K.
History
DepositionApr 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)356,7184
Polymers356,7184
Non-polymers00
Water00
1
A: CHOLINE TRIMETHYLAMINE LYASE
B: CHOLINE TRIMETHYLAMINE LYASE


Theoretical massNumber of molelcules
Total (without water)178,3592
Polymers178,3592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10.3 kcal/mol
Surface area55360 Å2
MethodPISA
2
C: CHOLINE TRIMETHYLAMINE LYASE
D: CHOLINE TRIMETHYLAMINE LYASE


Theoretical massNumber of molelcules
Total (without water)178,3592
Polymers178,3592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-8.4 kcal/mol
Surface area54430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.600, 154.550, 120.780
Angle α, β, γ (deg.)90.00, 96.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CHOLINE TRIMETHYLAMINE LYASE


Mass: 89179.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Description: THE MICROBIAL STRAIN COLLECTION OF LATVIA / Plasmid: PRSF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL45*PLUS

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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: 2.64 Å3/Da / Density % sol: 53.39 % / Description: NONE
Crystal growpH: 6.5
Details: 20% PEG 3350, 100-160 MM K/NA TARTRATE, 100 MM BIS-TRIS, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.984
DetectorType: RAYONIX BONDED TO FIBER-OPTIC TAPERS / Detector: CCD / Date: Feb 9, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3→61.78 Å / Num. obs: 66881 / % possible obs: 89.3 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 76.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A0U

5a0u


Resolution: 3→119.92 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.771 / Cross valid method: THROUGHOUT / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 937A-946A, 980A-984A, 1004A-1017A, 1027A-1039A, 909B- 916B, 939B-946B, 981B-984B, 1006B-1015B, 1026B-1041B, , 905C- 913C, 938C- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 937A-946A, 980A-984A, 1004A-1017A, 1027A-1039A, 909B- 916B, 939B-946B, 981B-984B, 1006B-1015B, 1026B-1041B, , 905C- 913C, 938C-944C, 980C-986C, 1007C-1016C, 1029C- -1041C, 902D- 946D, 983D-985D, 997D-1017D, 1029D-1041D ARE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY, SIDE CHAINS OF RESIDUES 662D, 675D, 769C, 773C, 771D, 799D, 803C, 804D, 808D, 821D, 822A, 822B, 822D, 892D, 897A, 898A, 900B, 901C, 918C, 923C, 934C, 935C, 948A, 950A, 952B, 952 D, 953B, 955A, 1000B, 1000C, 1025A, 1054B, 1054C, 1076D, 1079B,1083B, 1088D, 1089A, 1089D, 1093B, 1100D, 1113D, 1114D, 1118D, 1122D, 1122B ARE MUTATED TO ALANINE DUE TO INSUFFICIENT ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.28598 3342 5 %RANDOM
Rwork0.23232 ---
obs0.23501 63518 88.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.544 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0.39 Å2
2--1.48 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 3→119.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23177 0 0 0 23177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01923654
X-RAY DIFFRACTIONr_bond_other_d00.0222320
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.95631992
X-RAY DIFFRACTIONr_angle_other_deg3.821351293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.76552930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63623.8851112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.734154028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.04715173
X-RAY DIFFRACTIONr_chiral_restr0.110.23515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226785
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025450
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8193.81211786
X-RAY DIFFRACTIONr_mcbond_other1.8193.81211785
X-RAY DIFFRACTIONr_mcangle_it3.1385.70614694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3343.8311868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 203 -
Rwork0.312 3969 -
obs--74.82 %

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