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- PDB-7xrm: Ethanolamine ammonia-lyase complexed with AdoMeCbl -

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Basic information

Entry
Database: PDB / ID: 7xrm
TitleEthanolamine ammonia-lyase complexed with AdoMeCbl
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 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) / Aldolase-type TIM barrel
Similarity search - Domain/homology
COBALAMIN / Chem-FWK / AMMONIUM ION / 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: 2.13 Å
AuthorsShibata, N. / Toraya, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemistry / Year: 2022
Title: Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.
Authors: Shibata, N. / Higuchi, Y. / Krautler, B. / Toraya, T.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,67421
Polymers156,4344
Non-polymers4,24017
Water11,728651
1
A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules

A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules

A: Ethanolamine ammonia-lyase large subunit
B: Ethanolamine ammonia-lyase small subunit
C: Ethanolamine ammonia-lyase large subunit
D: Ethanolamine ammonia-lyase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,02263
Polymers469,30112
Non-polymers12,72151
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-y+2,x-y-1,z1
crystal symmetry operation3_875-x+y+3,-x+2,z1
Buried area62550 Å2
ΔGint-186 kcal/mol
Surface area123270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.885, 242.885, 76.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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

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


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


Mass: 28769.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutC, b2440, JW2433 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P19636, ethanolamine ammonia-lyase

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Non-polymers , 5 types, 668 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-FWK / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol


Mass: 265.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.17 Å3/Da / Density % sol: 70.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% (w/v) PEG 6000, 0.1 M ammonium chloride, and 0.05 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 2.13→47 Å / Num. obs: 143007 / % possible obs: 99.2 % / Redundancy: 7.71 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.132 / Net I/σ(I): 14.95
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 7.64 % / Rmerge(I) obs: 1.173 / Num. unique obs: 10603 / CC1/2: 0.479 / Rrim(I) all: 1.258 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABR

3abr


Resolution: 2.13→46.42 Å / Cross valid method: FREE R-VALUE / σ(F): 58.54 / Phase error: 26.0603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 7190 5.03 %
Rwork0.1942 135810 -
obs0.1962 143005 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.99 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10770 0 288 651 11709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003411356
X-RAY DIFFRACTIONf_angle_d0.887415458
X-RAY DIFFRACTIONf_chiral_restr0.04671769
X-RAY DIFFRACTIONf_plane_restr0.00472017
X-RAY DIFFRACTIONf_dihedral_angle_d9.22231713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.170.29773290.27886788X-RAY DIFFRACTION95.26
2.17-2.210.29544060.26446747X-RAY DIFFRACTION94
2.21-2.250.26823530.25456827X-RAY DIFFRACTION94.99
2.25-2.30.2773300.24816799X-RAY DIFFRACTION95.08
2.3-2.350.27823590.24446748X-RAY DIFFRACTION94.54
2.35-2.40.28553330.23666837X-RAY DIFFRACTION94.91
2.4-2.460.26723570.23076790X-RAY DIFFRACTION95
2.46-2.530.24543630.22486775X-RAY DIFFRACTION94.44
2.53-2.60.2523500.22436779X-RAY DIFFRACTION94.55
2.6-2.680.24473590.21816795X-RAY DIFFRACTION94.41
2.68-2.780.23633650.21296761X-RAY DIFFRACTION94.28
2.78-2.890.22353570.20796822X-RAY DIFFRACTION94.42
2.89-3.020.23493560.20236766X-RAY DIFFRACTION94.34
3.02-3.180.22343960.19596756X-RAY DIFFRACTION93.39
3.18-3.380.20763530.1866764X-RAY DIFFRACTION94.11
3.38-3.640.21123440.17946799X-RAY DIFFRACTION93.93
3.64-4.010.17443640.16426765X-RAY DIFFRACTION93.83
4.01-4.590.18583660.15066797X-RAY DIFFRACTION93.47
4.59-5.780.19293560.16526842X-RAY DIFFRACTION93.55
5.78-46.420.21713940.19536858X-RAY DIFFRACTION92.08
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)
11.22930018808-0.3360999210920.09202889656570.786718454632-0.06996617238560.4382393870080.05175331722340.177059681783-0.432093716836-0.0561536938726-0.01573012080740.07027149779060.1444361747460.0529922426166-0.01373428687110.3224478681520.0177440927713-0.0277358075220.149744667693-0.08136470342810.334566494415371.83443939733.8266508257-10.1757439296
20.312188959399-0.332566943997-0.1230340485440.9529164378370.2391216884170.07482304514270.07262083711210.50627079266-0.609286887577-0.313263782476-0.06262918948450.1600659151140.227189535658-0.0678506461382-0.01304799043180.6227463923930.0362707649985-0.08422762664570.377696383283-0.4014570808830.814509714683366.95915554514.1006706629-28.4365487814
31.50869845484-0.2650746907020.1095992404280.8455963417870.02020542924170.825513850345-0.0141483184470.0201806747948-0.448087112240.02227243030390.02973068750690.2548412980250.141716082209-0.2017286096570.004478325567590.230822915148-0.0314762919594-0.009547693966030.1846268782260.01283631134870.344593356068337.32884221644.4763606226-4.36761011448
40.667074397328-0.082155078163-0.4079295670760.89980640337-0.1363345950611.3203299228-0.0858321407875-0.385627428908-0.7469060797360.2216107689780.08735903230840.4764373901790.437257730601-0.697094955594-0.01954112874190.598059160398-0.1287928297290.1201923659870.6736984050560.275435696370.941662297846330.13266212225.23195639713.9193289839
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 453)AA1 - 4531 - 453
22(chain 'B' and (resid 43 through 295 or resid 601))BB - C43 - 6011
33(chain 'C' and resid 1 through 453)CD1 - 4531 - 453
44(chain 'D' and (resid 44 through 295 or resid 601))DE - F44 - 6011

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