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Basic information

Entry
Database: PDB / ID: 3abo
TitleCrystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and ethanolamine
Components(Ethanolamine ammonia-lyase ...) x 2
KeywordsLYASE / (beta/alpha)8 fold / Cobalt / Cobalamin
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
Helix Hairpins - #690 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2060 / 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 ...Helix Hairpins - #690 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2060 / 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 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 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
COBALAMIN / ETHANOLAMINE / Ethanolamine ammonia-lyase large subunit / Ethanolamine ammonia-lyase small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 2.1 Å
AuthorsShibata, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.
Authors: Shibata, N. / Tamagaki, H. / Hieda, N. / Akita, K. / Komori, H. / Shomura, Y. / Terawaki, S. / Mori, K. / Yasuoka, N. / Higuchi, Y. / Toraya, T.
History
DepositionDec 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Feb 19, 2014Group: Database references / Derived calculations
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)168,57915
Polymers165,2904
Non-polymers3,28911
Water12,737707
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)505,73745
Polymers495,86912
Non-polymers9,86833
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
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-53 kcal/mol
Surface area44510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.760, 242.760, 76.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D
/ NCS ensembles :
ID
1
2

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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 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: b2441, eutB, JW2434 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase
#2: Protein Ethanolamine ammonia-lyase light chain / / Ethanolamine ammonia-lyase small subunit


Mass: 33197.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2440, eutC, JW2433 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19636, ethanolamine ammonia-lyase

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Non-polymers , 5 types, 718 molecules

#3: Chemical ChemComp-ETA / ETHANOLAMINE / Ethanolamine


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6.0-7.0 % (w/v) PEG 6000, 24-26 % (v/v) glycerol, 5.0 % (v/v) 2-propanol, 0.1 M HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 11, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 145836 / Num. obs: 145836 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.35 / Num. unique all: 9228 / % possible all: 93.1

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Processing

Software
NameVersionClassification
SHARPphasing
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: PDB ENTRY 2QEZ

2qez


Resolution: 2.1→47.51 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.138 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 7304 5 %RANDOM
Rwork0.23966 ---
obs0.24099 138458 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10735 0 222 707 11664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.99315119
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.63251400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00924.351485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.292151877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7761584
X-RAY DIFFRACTIONr_chiral_restr0.260.21744
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218352
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1291.56970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.737211198
X-RAY DIFFRACTIONr_scbond_it3.37134158
X-RAY DIFFRACTIONr_scangle_it4.8094.53921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1780tight positional0.050.05
11C1615medium positional0.20.5
22B1093medium positional0.30.5
22D685loose positional0.295
11A1780tight thermal0.330.5
11C1615medium thermal0.392
22B1093medium thermal3.392
22D685loose thermal3.2310
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 535 -
Rwork0.252 9702 -
obs--93 %
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)
10.4912-0.1459-0.09691.65320.00170.33460.06610.0504-0.1169-0.2087-0.02420.4470.02920.0248-0.04190.0937-0.0412-0.08960.1204-0.01160.15494.013-94.827-8.341
20.89980.3305-0.17752.0052-0.03790.20220.06870.2285-0.1815-0.8026-0.04671.04880.0427-0.0848-0.02210.4701-0.0214-0.55980.2727-0.11780.80574.0632-100.4146-27.2475
30.4179-0.24790.04151.8781-0.12160.5240.03710.0279-0.03840.04490.01550.6212-0.0718-0.0463-0.05260.0847-0.01030.01870.12420.02840.220485.914-59.715-2.681
41.1709-0.40440.07682.8068-0.55371.3399-0.1088-0.2329-0.15160.83840.41751.7991-0.393-0.5179-0.30860.47840.13350.59260.3830.18881.375265.484-63.7915.823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 453
2X-RAY DIFFRACTION2B44 - 295
3X-RAY DIFFRACTION3C1 - 453
4X-RAY DIFFRACTION4D44 - 295

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