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- PDB-6tor: human O-phosphoethanolamine phospho-lyase -

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Basic information

Entry
Database: PDB / ID: 6tor
Titlehuman O-phosphoethanolamine phospho-lyase
ComponentsEthanolamine-phosphate phospho-lyase
KeywordsLYASE / O-phosphoethanolamine phospho-lyase / pyridoxal 5'-phosphate-dependent enzyme / phospholipid metabolism.
Function / homology
Function and homology information


ethanolamine-phosphate phospho-lyase / ethanolamine-phosphate phospho-lyase activity / Synthesis of PE / transaminase activity / pyridoxal phosphate binding / mitochondrial matrix
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Ethanolamine-phosphate phospho-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVettraino, C. / Donini, S. / Parisini, E.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of human O-phosphoethanolamine phospho-lyase.
Authors: Vettraino, C. / Peracchi, A. / Donini, S. / Parisini, E.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of human O-phosphoethanolamine phospho-lyase.
Authors: Vettraino, C. / Peracchi, S. / Donini, S. / Parisini, E.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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-phosphate phospho-lyase
B: Ethanolamine-phosphate phospho-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,56410
Polymers111,5162
Non-polymers1,0498
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-24 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.998, 137.998, 121.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ethanolamine-phosphate phospho-lyase / Alanine--glyoxylate aminotransferase 2-like 1


Mass: 55757.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETNPPL, AGXT2L1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TBG4, ethanolamine-phosphate phospho-lyase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 100 mM Bis Tris propane pH 7.0, 200 mM ammonium sulfate, and 3% MPD.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→69.09 Å / Num. obs: 54318 / % possible obs: 99.99 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.068 / Net I/σ(I): 10.1
Reflection shellResolution: 2.05→2.16 Å / Rmerge(I) obs: 0.102 / Num. unique obs: 54318

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHASERmodel building
SCALAdata scaling
MOSFLMdata processing
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4I

5g4i


Resolution: 2.05→69.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.186 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 2812 5.2 %RANDOM
Rwork0.1631 ---
obs0.165 51478 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.21 Å2 / Biso mean: 21 Å2 / Biso min: 4.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å2-0 Å2
2--0.44 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 2.05→69.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 68 571 6935
Biso mean--49.06 29.98 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136486
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176051
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6458743
X-RAY DIFFRACTIONr_angle_other_deg1.3851.58314047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59322.831332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.957151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8551534
X-RAY DIFFRACTIONr_chiral_restr0.0790.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021317
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 206 -
Rwork0.219 3820 -
all-4026 -
obs--100 %

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