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- PDB-5ysn: Ethanolamine ammonia-lyase, AdoCbl/substrate-free -

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Basic information

Entry
Database: PDB / ID: 5ysn
TitleEthanolamine ammonia-lyase, AdoCbl/substrate-free
Components(Ethanolamine ammonia-lyase ...) x 2
KeywordsLYASE / Adenosylcobalamin / Radical enzyme
Function / homology
Function and homology information


ethanolamine ammonia-lyase / ethanolamine ammonia-lyase activity / ethanolamine ammonia-lyase complex / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / cobalamin binding / amino acid metabolic process / cytosol
Similarity search - Function
Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / lyase / ethanolamine ammonia-lyase heavy chain domain like / Ethanolamine ammonia-lyase small subunit / Ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia-lyase light chain, C-terminal / Ethanolamine ammonia-lyase heavy chain, domain 2 / Ethanolamine ammonia-lyase heavy chain, N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) ...Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / lyase / ethanolamine ammonia-lyase heavy chain domain like / Ethanolamine ammonia-lyase small subunit / Ethanolamine ammonia-lyase heavy chain / Ethanolamine ammonia-lyase light chain, C-terminal / Ethanolamine ammonia-lyase heavy chain, domain 2 / Ethanolamine ammonia-lyase heavy chain, N-terminal domain / Ethanolamine ammonia-lyase light chain (EutC) / Ethanolamine ammonia lyase large subunit (EutB) / DNA Binding (I), subunit A / Ribosomal Protein L24e; Chain: T; / Annexin V; domain 1 / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / Ethanolamine ammonia-lyase large subunit / Ethanolamine ammonia-lyase small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsShibata, N.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.
Authors: Shibata, N. / Sueyoshi, Y. / Higuchi, Y. / Toraya, T.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,71119
Polymers162,5354
Non-polymers4,17615
Water17,745985
1
A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules

A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules

A: Ethanolamine ammonia-lyase heavy chain
B: Ethanolamine ammonia-lyase light chain
C: Ethanolamine ammonia-lyase heavy chain
D: Ethanolamine ammonia-lyase light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,13357
Polymers487,60412
Non-polymers12,52945
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area64100 Å2
ΔGint-181 kcal/mol
Surface area123450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.723, 242.723, 76.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Ethanolamine ammonia-lyase ... , 2 types, 4 molecules ACBD

#1: Protein Ethanolamine ammonia-lyase heavy chain / / Ethanolamine ammonia-lyase alpha subunit / Ethanolamine ammonia-lyase large subunit


Mass: 49447.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: eutB, b2441, JW2434 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase
#2: Protein Ethanolamine ammonia-lyase light chain / / Ethanolamine ammonia-lyase beta subunit / Ethanolamine ammonia-lyase small subunit


Mass: 31819.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: eutC, b2440, JW2433 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P19636, ethanolamine ammonia-lyase

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Non-polymers , 4 types, 1000 molecules

#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 4.01 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 12.5% (w/v) PEG 1500, 0.05M sodium malonate, imidazole, boric acid (MIB) buffer pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→48 Å / Num. obs: 172666 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.11 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 8189 / CC1/2: 0.59 / Rrim(I) all: 0.643 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABR

3abr


Resolution: 2.001→48 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.63
RfactorNum. reflection% reflection
Rfree0.1917 8663 5.02 %
Rwork0.1633 --
obs0.1649 172653 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 284 985 12029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911357
X-RAY DIFFRACTIONf_angle_d1.2415466
X-RAY DIFFRACTIONf_dihedral_angle_d19.3736929
X-RAY DIFFRACTIONf_chiral_restr0.0591771
X-RAY DIFFRACTIONf_plane_restr0.0062021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0017-2.03620.26344050.247670X-RAY DIFFRACTION89
2.0362-2.07320.24614270.22568059X-RAY DIFFRACTION93
2.0732-2.11310.24684110.21218159X-RAY DIFFRACTION95
2.1131-2.15620.25393880.2098254X-RAY DIFFRACTION96
2.1562-2.20310.21974690.2028107X-RAY DIFFRACTION95
2.2031-2.25440.20054310.19548229X-RAY DIFFRACTION95
2.2544-2.31070.22044090.19448210X-RAY DIFFRACTION95
2.3107-2.37320.22554120.18958215X-RAY DIFFRACTION95
2.3732-2.4430.22774280.18728191X-RAY DIFFRACTION95
2.443-2.52180.18924400.18268203X-RAY DIFFRACTION95
2.5218-2.61190.21734200.17918232X-RAY DIFFRACTION95
2.6119-2.71640.22634300.17528219X-RAY DIFFRACTION95
2.7164-2.840.20714530.17118198X-RAY DIFFRACTION95
2.84-2.98960.19694290.16698232X-RAY DIFFRACTION95
2.9896-3.17680.18134670.15958204X-RAY DIFFRACTION95
3.1768-3.42180.18444280.14988261X-RAY DIFFRACTION95
3.4218-3.76570.16674230.13548255X-RAY DIFFRACTION95
3.7657-4.30950.1564410.1248292X-RAY DIFFRACTION95
4.3095-5.42540.14834460.12358325X-RAY DIFFRACTION95
5.4254-32.38420.18044790.15568452X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 94.598 Å / Origin y: -98.7254 Å / Origin z: -26.796 Å
111213212223313233
T0.1739 Å2-0.0934 Å20.004 Å2-0.2164 Å20.0492 Å2--0.2648 Å2
L0.9598 °2-0.5372 °20.0523 °2-0.6551 °2-0.0371 °2--0.3936 °2
S0.0043 Å °-0.0352 Å °-0.3842 Å °0.0387 Å °0.0485 Å °0.3038 Å °0.1454 Å °-0.0834 Å °0.0159 Å °
Refinement TLS groupSelection details: all

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