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- PDB-3mc6: Crystal structure of ScDPL1 -

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Basic information

Entry
Database: PDB / ID: 3mc6
TitleCrystal structure of ScDPL1
Components(Sphingosine-1-phosphate lyaseSGPL1) x 2
KeywordsLYASE / carboxy-lyase activity / pyridoxyl phosphate
Function / homology
Function and homology information


sphinganine-1-phosphate aldolase / sphinganine-1-phosphate aldolase activity / Sphingolipid de novo biosynthesis / Lyases; Carbon-carbon lyases; Aldehyde-lyases / sphingolipid catabolic process / cortical endoplasmic reticulum / perinuclear endoplasmic reticulum / sphingolipid metabolic process / carboxy-lyase activity / carboxylic acid metabolic process ...sphinganine-1-phosphate aldolase / sphinganine-1-phosphate aldolase activity / Sphingolipid de novo biosynthesis / Lyases; Carbon-carbon lyases; Aldehyde-lyases / sphingolipid catabolic process / cortical endoplasmic reticulum / perinuclear endoplasmic reticulum / sphingolipid metabolic process / carboxy-lyase activity / carboxylic acid metabolic process / cellular response to starvation / calcium-mediated signaling / pyridoxal phosphate binding / endoplasmic reticulum / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3090 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3090 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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
PHOSPHATE ION / Sphingosine-1-phosphate lyase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBourquin, F. / Grutter, M.G. / Capitani, G.
CitationJournal: Structure / Year: 2010
Title: Structure and Function of Sphingosine-1-Phosphate Lyase, a Key Enzyme of Sphingolipid Metabolism.
Authors: Bourquin, F. / Riezman, H. / Capitani, G. / Grutter, M.G.
History
DepositionMar 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sphingosine-1-phosphate lyase
C: Sphingosine-1-phosphate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8665
Polymers109,5812
Non-polymers2853
Water724
1
A: Sphingosine-1-phosphate lyase
hetero molecules

A: Sphingosine-1-phosphate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9994
Polymers109,8092
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12670 Å2
ΔGint-100 kcal/mol
Surface area30710 Å2
MethodPISA
2
C: Sphingosine-1-phosphate lyase
hetero molecules

C: Sphingosine-1-phosphate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7336
Polymers109,3532
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_445-x-1/2,-y-1/2,z1
Buried area13080 Å2
ΔGint-116 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.100, 156.860, 201.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 131:379 or resseq 381:540 or resseq 564:579 )
211chain C and (resseq 131:379 or resseq 381:540 or resseq 567:579 )

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Components

#1: Protein Sphingosine-1-phosphate lyase / SGPL1 / SP-lyase / ySPL / Sphingosine-1-phosphate aldolase / Bestowed of sphingosine tolerance 1


Mass: 54904.539 Da / Num. of mol.: 1 / Fragment: Residues 103-589 / Mutation: I308V, N469D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BST1, D9819.5, DPL1, YDR294C / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q05567, sphinganine-1-phosphate aldolase
#2: Protein Sphingosine-1-phosphate lyase / SGPL1 / SP-lyase / ySPL / Sphingosine-1-phosphate aldolase / Bestowed of sphingosine tolerance 1


Mass: 54676.422 Da / Num. of mol.: 1 / Fragment: Residues 103-589 / Mutation: I308V, N469D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BST1, D9819.5, DPL1, YDR294C / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q05567, sphinganine-1-phosphate aldolase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.73 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / pH: 6.7
Details: PEG 4000 18%, 0.1 M Na-cacodylate (HOAc) pH 6.7, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2007 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.15→47.99 Å / Num. obs: 20848 / % possible obs: 99.9 % / Redundancy: 6.52 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.1
Reflection shellResolution: 3.15→3.32 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED MODEL OF STSPL MUTANT K311A (DIMERIC)

Resolution: 3.15→41.92 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / Isotropic thermal model: ISOTROPIC / Phase error: 34.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3 610 2.95 %
Rwork0.241 --
obs0.243 20686 99.2 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.05 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 127.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.973 Å2-0 Å2-0 Å2
2---2.96 Å2-0 Å2
3---0.987 Å2
Refinement stepCycle: LAST / Resolution: 3.15→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6615 0 15 4 6634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026784
X-RAY DIFFRACTIONf_angle_d0.5229196
X-RAY DIFFRACTIONf_dihedral_angle_d11.842444
X-RAY DIFFRACTIONf_chiral_restr0.0371020
X-RAY DIFFRACTIONf_plane_restr0.0021171
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3280X-RAY DIFFRACTIONPOSITIONAL
12C3280X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.4670.3671520.2894959X-RAY DIFFRACTION99
3.467-3.9680.3771490.2614946X-RAY DIFFRACTION99
3.968-4.9980.3261520.244989X-RAY DIFFRACTION99
4.998-41.9290.2381570.2185182X-RAY DIFFRACTION100

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