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- PDB-5eue: S1P Lyase Bacterial Surrogate bound to N-(2-((4-methoxy-2,5-dimet... -

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Basic information

Entry
Database: PDB / ID: 5eue
TitleS1P Lyase Bacterial Surrogate bound to N-(2-((4-methoxy-2,5-dimethylbenzyl)amino)-1-phenylethyl)-5-methylisoxazole-3-carboxamide
ComponentsPutative sphingosine-1-phosphate lyaseSGPL1
KeywordsLYASE / S1P Lyase bacterial surrogate
Function / homology
Function and homology information


aromatic-L-amino-acid decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
Helix Hairpins - #2150 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Helix Hairpins / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Helix non-globular / Pyridoxal phosphate-dependent transferase, small domain ...Helix Hairpins - #2150 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Helix Hairpins / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Helix non-globular / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Special / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5S5 / PHOSPHATE ION / Putative sphingosine-1-phosphate lyase
Similarity search - Component
Biological speciesSymbiobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsArgiriadi, M.A. / Banach, D. / Radziejewska, E. / Marchie, S. / DiMauro, J. / Dinges, J. / Dominguez, E. / Hutchins, C. / Judge, R.A. / Queeney, K. ...Argiriadi, M.A. / Banach, D. / Radziejewska, E. / Marchie, S. / DiMauro, J. / Dinges, J. / Dominguez, E. / Hutchins, C. / Judge, R.A. / Queeney, K. / Wallace, G. / Harris, C.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Creation of a S1P Lyase bacterial surrogate for structure-based drug design.
Authors: Argiriadi, M.A. / Banach, D. / Radziejewska, E. / Marchie, S. / DiMauro, J. / Dinges, J. / Dominguez, E. / Hutchins, C. / Judge, R.A. / Queeney, K. / Wallace, G. / Harris, C.M.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 27, 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_oper_list / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _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: Putative sphingosine-1-phosphate lyase
B: Putative sphingosine-1-phosphate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4596
Polymers111,4822
Non-polymers9774
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-119 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.014, 129.606, 84.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative sphingosine-1-phosphate lyase / SGPL1


Mass: 55741.043 Da / Num. of mol.: 2 / Mutation: Y249F, L344I, F346A, L497S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Symbiobacterium thermophilum (strain T / IAM 14863) (bacteria)
Strain: T / IAM 14863 / Gene: STH1274 / Production host: Escherichia coli (E. coli) / References: UniProt: Q67PY4
#2: Chemical ChemComp-5S5 / ~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-phenyl-ethyl]-5-methyl-1,2-oxazole-3-carboxamide


Mass: 393.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N3O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 0.15 M KCSN, 0.1M Tris, pH 8.3, 18% PEG 5000 MME / PH range: 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→129.6 Å / Num. obs: 22823 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 61.86 Å2 / Rsym value: 0.11 / Net I/σ(I): 15.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MAD

3mad


Resolution: 2.83→71.09 Å / Cor.coef. Fo:Fc: 0.9363 / Cor.coef. Fo:Fc free: 0.8725 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.387
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 1168 5.13 %RANDOM
Rwork0.173 ---
obs0.1768 22754 99.59 %-
Displacement parametersBiso mean: 46.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.7032 Å20 Å20 Å2
2---2.5765 Å20 Å2
3---0.8733 Å2
Refine analyzeLuzzati coordinate error obs: 0.288 Å
Refinement stepCycle: LAST / Resolution: 2.83→71.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6784 0 68 126 6978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017096HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.149699HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2238SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1091HARMONIC5
X-RAY DIFFRACTIONt_it7096HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion901SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8498SEMIHARMONIC4
LS refinement shellResolution: 2.83→2.97 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2702 155 5.3 %
Rwork0.1877 2767 -
all0.192 2922 -
obs--99.59 %

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