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- PDB-4w8i: Crystal structure of LpSPL/Lpp2128, Legionella pneumophila sphing... -

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Basic information

Entry
Database: PDB / ID: 4w8i
TitleCrystal structure of LpSPL/Lpp2128, Legionella pneumophila sphingosine-1 phosphate lyase
ComponentsProbable sphingosine-1-phosphate lyase
KeywordsLYASE / effector / structural genomics / PSI-Biology / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


sphinganine-1-phosphate aldolase / sphinganine-1-phosphate aldolase activity / carboxy-lyase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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 ...Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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
Probable sphingosine-1-phosphate lyase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsStogios, P.J. / Daniels, C. / Skarina, T. / Cuff, M. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy.
Authors: Rolando, M. / Escoll, P. / Nora, T. / Botti, J. / Boitez, V. / Bedia, C. / Daniels, C. / Abraham, G. / Stogios, P.J. / Skarina, T. / Christophe, C. / Dervins-Ravault, D. / Cazalet, C. / ...Authors: Rolando, M. / Escoll, P. / Nora, T. / Botti, J. / Boitez, V. / Bedia, C. / Daniels, C. / Abraham, G. / Stogios, P.J. / Skarina, T. / Christophe, C. / Dervins-Ravault, D. / Cazalet, C. / Hilbi, H. / Rupasinghe, T.W. / Tull, D. / McConville, M.J. / Ong, S.Y. / Hartland, E.L. / Codogno, P. / Levade, T. / Naderer, T. / Savchenko, A. / Buchrieser, C.
History
DepositionAug 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 17, 2016Group: Data collection
Revision 1.3Mar 2, 2016Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Mar 13, 2024Group: Atomic model / Data collection / Category: atom_site / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable sphingosine-1-phosphate lyase
B: Probable sphingosine-1-phosphate lyase


Theoretical massNumber of molelcules
Total (without water)121,6752
Polymers121,6752
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-44 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.783, 118.252, 57.794
Angle α, β, γ (deg.)90.00, 114.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable sphingosine-1-phosphate lyase / SPL / Sphingosine-1-phosphate aldolase


Mass: 60837.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Paris / Gene: lpp2128 / Plasmid: p19MBP-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5X3A8, sphinganine-1-phosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.1 M sodium chloride, 0.1 M potassium chloride, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.46→20 Å / Num. obs: 25700 / % possible obs: 99.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 43.63 Å2 / Rsym value: 0.073 / Net I/σ(I): 20.56
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.04 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphenix.autosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→19.709 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.96 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3162 1471 5.05 %random selection
Rwork0.2624 ---
obs0.2654 16318 89.83 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→19.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 0 16 5515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075605
X-RAY DIFFRACTIONf_angle_d1.3257594
X-RAY DIFFRACTIONf_dihedral_angle_d15.7362014
X-RAY DIFFRACTIONf_chiral_restr0.054878
X-RAY DIFFRACTIONf_plane_restr0.007967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.95180.36381360.32152535X-RAY DIFFRACTION83
2.9518-3.06960.33591460.31922619X-RAY DIFFRACTION85
3.0696-3.20870.42431480.30122702X-RAY DIFFRACTION87
3.2087-3.37710.30251370.29232718X-RAY DIFFRACTION88
3.3771-3.58750.35681440.27432781X-RAY DIFFRACTION91
3.5875-3.86260.31961460.26122836X-RAY DIFFRACTION92
3.8626-4.24780.30921530.25382828X-RAY DIFFRACTION92
4.2478-4.85440.29731490.2322869X-RAY DIFFRACTION93
4.8544-6.0860.2811560.24412837X-RAY DIFFRACTION93
6.086-19.70910.29341560.2422944X-RAY DIFFRACTION95
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)
11.054-0.87810.171.8244-0.0160.03870.09810.09050.3559-0.3701-0.2435-0.3403-0.05340.2283-0.05850.14670.01780.22620.56680.04630.7224-5.942281.778620.6179
24.2375-0.3132-1.77711.71710.02092.33540.03210.08690.0863-0.05290.021-0.0031-0.0972-0.1094-0.05930.18110.00050.08620.21820.00130.3407-29.855363.242732.9851
32.02980.2761-0.55261.16080.31473.71650.2801-0.3499-0.06610.09790.0923-0.2709-0.41250.4397-0.1005-0.26440.09430.31990.2649-0.01790.2073-7.64759.292950.1055
41.87420.3747-0.68065.2149-0.93073.219-0.10890.62690.1212-0.50250.0715-0.11140.1951-0.43710.04110.26320.02670.21240.58340.00390.5511-9.358672.745112.1789
56.58010.3093-1.93011.1952-0.4642.686-0.0964-0.3526-0.08160.03810.0774-0.13940.06160.16680.00990.2651-0.01920.13160.2773-0.02840.5016-31.864694.686827.6565
62.58190.0578-1.50023.21011.61823.8622-0.05661.3527-0.6036-0.6937-0.19810.5484-0.4079-0.6322-0.04080.24590.11260.24790.8587-0.08370.7827-37.245795.36020.708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 108:180
2X-RAY DIFFRACTION2chain A and resi 192:429
3X-RAY DIFFRACTION3chain A and resi 430:529
4X-RAY DIFFRACTION4chain B and resi 107:179
5X-RAY DIFFRACTION5chain B and resi 191:429
6X-RAY DIFFRACTION6chain B and resi 430:526

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