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- PDB-5a0u: Structure of CutC choline lyase choline bound form from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 5a0u
TitleStructure of CutC choline lyase choline bound 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 ION / Choline trimethylamine-lyase
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly ...diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[3]
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
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)716,64916
Polymers715,8158
Non-polymers8338
Water35,5981976
1
A: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules

G: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1624
Polymers178,9542
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area3240 Å2
ΔGint5 kcal/mol
Surface area48830 Å2
MethodPISA
2
B: CHOLINE TRIMETHYLAMINE LYASE
H: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1624
Polymers178,9542
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint5 kcal/mol
Surface area48770 Å2
MethodPISA
3
C: CHOLINE TRIMETHYLAMINE LYASE
D: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1624
Polymers178,9542
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint6 kcal/mol
Surface area48800 Å2
MethodPISA
4
E: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules

F: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1624
Polymers178,9542
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area3310 Å2
ΔGint6 kcal/mol
Surface area48880 Å2
MethodPISA
5
F: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules

E: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1624
Polymers178,9542
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
6
G: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules

A: CHOLINE TRIMETHYLAMINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1624
Polymers178,9542
Non-polymers2082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Unit cell
Length a, b, c (Å)89.410, 221.870, 419.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CHOLINE TRIMETHYLAMINE LYASE


Mass: 89476.922 Da / Num. of mol.: 8 / Fragment: RESIDUES 334-1028
Source method: isolated from a genetically manipulated source
Details: N_TERMINUS CLEAVED WITH CHYMOTRYPSN LEAVING VARIABLE N-TERMINAL SEQUENCE
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: A0A0M3KL44*PLUS
#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H14NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1976 / 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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: NONE
Crystal growpH: 8.5
Details: 20% PEG 3350, 60-20 MM K/NA TARTRATE, 100 MM BIS-TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: RAYONIX / Detector: CCD / Date: Dec 12, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→209.74 Å / Num. obs: 289262 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.8 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R9D

1r9d


Resolution: 2.4→209.74 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.181 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24699 15197 5 %RANDOM
Rwork0.18787 ---
obs0.19083 289262 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.181 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2---1.62 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→209.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50095 0 56 1976 52127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01951192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248660
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.96169276
X-RAY DIFFRACTIONr_angle_other_deg0.8783111932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74456337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35923.9932424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.342158896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.40515376
X-RAY DIFFRACTIONr_chiral_restr0.0920.27577
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02158176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211776
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_it1.4482.72425372
X-RAY DIFFRACTIONr_mcbond_other1.4482.72425371
X-RAY DIFFRACTIONr_mcangle_it2.2974.08231701
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6472.91925820
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6884.337576
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 1023 -
Rwork0.294 19910 -
obs--87.81 %

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