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- PDB-5ysr: Ethanolamine ammonia-lyase, AdoCbl/2-amino-1-propanol -

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Basic information

Entry
Database: PDB / ID: 5ysr
TitleEthanolamine ammonia-lyase, AdoCbl/2-amino-1-propanol
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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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

Downloads & links

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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
Water11,602644
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 area61490 Å2
ΔGint-177 kcal/mol
Surface area123920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.500, 242.500, 77.020
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 K-12 (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 K-12 (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, 659 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.: 644 / 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: 4.02 Å3/Da / Density % sol: 69.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% (w/v) PEG 6000, 0.1M ammonium chloride, 0.05M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.75
ReflectionResolution: 2.05→48 Å / Num. obs: 161685 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.121 / Net I/σ(I): 15.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 11915 / CC1/2: 0.503 / Rrim(I) all: 0.764 / % possible all: 100

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Processing

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

3abr


Resolution: 2.05→48 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.53 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2566 8084 5.24 %
Rwork0.2227 --
obs0.2451 161685 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10749 0 284 644 11677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611319
X-RAY DIFFRACTIONf_angle_d1.07115413
X-RAY DIFFRACTIONf_dihedral_angle_d19.9696896
X-RAY DIFFRACTIONf_chiral_restr0.051765
X-RAY DIFFRACTIONf_plane_restr0.0052013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08540.32347520.289614154X-RAY DIFFRACTION89
2.0854-2.12330.32476940.292814201X-RAY DIFFRACTION90
2.1233-2.16410.30137000.284714258X-RAY DIFFRACTION90
2.1641-2.20830.31788310.282414197X-RAY DIFFRACTION89
2.2083-2.25630.30247390.27814199X-RAY DIFFRACTION90
2.2563-2.30880.30297120.276214386X-RAY DIFFRACTION90
2.3088-2.36650.30237640.271614197X-RAY DIFFRACTION90
2.3665-2.43050.30887070.265414456X-RAY DIFFRACTION90
2.4305-2.50190.28637730.261814291X-RAY DIFFRACTION90
2.5019-2.58270.29247480.253514356X-RAY DIFFRACTION90
2.5827-2.67490.28197600.252314352X-RAY DIFFRACTION90
2.6749-2.7820.27437810.244514358X-RAY DIFFRACTION90
2.782-2.90850.28257570.245114408X-RAY DIFFRACTION91
2.9085-3.06170.28817800.241914466X-RAY DIFFRACTION91
3.0617-3.25340.28057760.239514444X-RAY DIFFRACTION91
3.2534-3.50430.2717500.238614491X-RAY DIFFRACTION91
3.5043-3.85650.26127720.234714515X-RAY DIFFRACTION91
3.8565-4.41340.24287940.220114490X-RAY DIFFRACTION91
4.4134-5.55580.23467500.211114569X-RAY DIFFRACTION92
5.5558-32.51040.26488370.228414571X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 94.56 Å / Origin y: -98.8337 Å / Origin z: -26.8922 Å
111213212223313233
T0.1168 Å2-0.0691 Å20.0154 Å2-0.1495 Å20.0376 Å2--0.2407 Å2
L0.5722 °2-0.2679 °2-0.0155 °2-0.4711 °2-0.0026 °2--0.2878 °2
S-0.0074 Å °-0.0442 Å °-0.2458 Å °0.0493 Å °0.025 Å °0.2243 Å °0.1066 Å °-0.0771 Å °0.0113 Å °
Refinement TLS groupSelection details: all

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