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- PDB-8cmx: Structure of sphingosine-1-phosphate lyase (SPL) from Aspergillus... -

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Basic information

Entry
Database: PDB / ID: 8cmx
TitleStructure of sphingosine-1-phosphate lyase (SPL) from Aspergillus fumigatus
ComponentsSphinganine-1-phosphate aldolase BST1, putative
KeywordsLYASE / sphingosine / sphingosine-1-phosphate / S1P
Function / homology
Function and homology information


sphinganine-1-phosphate aldolase / sphinganine-1-phosphate aldolase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / carboxylic acid metabolic process / sphingolipid catabolic process / cellular response to starvation / calcium-mediated signaling / pyridoxal phosphate binding / endoplasmic reticulum / identical protein binding
Similarity search - Function
: / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
sphinganine-1-phosphate aldolase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsCatalano, F. / Pampalone, G.
Funding support3items
OrganizationGrant numberCountry
Other governmentRP11916B407928AA
Other governmentRM12117A5BDD4AEC
Other privateFFC#16/2020
CitationJournal: Sci Rep / Year: 2023
Title: Dual species sphingosine-1-phosphate lyase inhibitors to combine antifungal and anti-inflammatory activities in cystic fibrosis: a feasibility study.
Authors: Cellini, B. / Pampalone, G. / Camaioni, E. / Pariano, M. / Catalano, F. / Zelante, T. / Dindo, M. / Macchioni, L. / Di Veroli, A. / Galarini, R. / Paoletti, F. / Davidescu, M. / Stincardini, ...Authors: Cellini, B. / Pampalone, G. / Camaioni, E. / Pariano, M. / Catalano, F. / Zelante, T. / Dindo, M. / Macchioni, L. / Di Veroli, A. / Galarini, R. / Paoletti, F. / Davidescu, M. / Stincardini, C. / Vascelli, G. / Bellet, M.M. / Saba, J. / Giovagnoli, S. / Giardina, G. / Romani, L. / Costantini, C.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphinganine-1-phosphate aldolase BST1, putative
B: Sphinganine-1-phosphate aldolase BST1, putative


Theoretical massNumber of molelcules
Total (without water)109,2022
Polymers109,2022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-99 kcal/mol
Surface area35510 Å2
Unit cell
Length a, b, c (Å)130.070, 130.070, 234.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Sphinganine-1-phosphate aldolase BST1, putative


Mass: 54601.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing 81 residues at N-terminal / Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: AFUA_4G10470 / Production host: Escherichia coli (E. coli) / Variant (production host): Delta-N 81
References: UniProt: Q4WPU3, sphinganine-1-phosphate aldolase
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.34 % / Description: hexagonal yellow crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes sodium pH 7.5 1.4 M Sodium citrate tribasic dihydrate DMSO 1% Cryoprotection = mother liquor + 20% Glycerol AfuSPL = 93 microM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.46→101.5 Å / Num. obs: 12600 / % possible obs: 95.1 % / Redundancy: 36.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.317 / Net I/σ(I): 15.1
Reflection shellResolution: 3.46→3.74 Å / Redundancy: 39 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 631 / CC1/2: 0.572 / % possible all: 71.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.46→100.02 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.897 / SU B: 51.092 / SU ML: 0.724 / Cross valid method: THROUGHOUT / ESU R Free: 0.918 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29551 1205 9.6 %RANDOM
Rwork0.28351 ---
obs0.28465 11394 79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 121.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å2-0 Å2
2---0.19 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: 1 / Resolution: 3.46→100.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 0 0 0 7343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167145
X-RAY DIFFRACTIONr_angle_refined_deg0.891.64610219
X-RAY DIFFRACTIONr_angle_other_deg0.3081.56716499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4095960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.556540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12101196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0410.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021632
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_it3.59112.1573852
X-RAY DIFFRACTIONr_mcbond_other3.58812.1563851
X-RAY DIFFRACTIONr_mcangle_it6.17921.8454808
X-RAY DIFFRACTIONr_mcangle_other6.17821.8454809
X-RAY DIFFRACTIONr_scbond_it3.75812.4493665
X-RAY DIFFRACTIONr_scbond_other3.75712.4493666
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.49422.7995412
X-RAY DIFFRACTIONr_long_range_B_refined10.65127.469298
X-RAY DIFFRACTIONr_long_range_B_other10.65127.469298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDNumberRms dev position (Å)
11206710.04
22155818.97
LS refinement shellResolution: 3.461→3.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 6 -
Rwork0.405 60 -
obs--5.81 %

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