[English] 日本語
Yorodumi
- PDB-8ayf: Crystal structure of human Sphingosine-1-phosphate lyase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ayf
TitleCrystal structure of human Sphingosine-1-phosphate lyase 1
ComponentsSphingosine-1-phosphate lyase 1
KeywordsLYASE / S1P / lipid
Function / homology
Function and homology information


Sphingolipid metabolism / sphinganine-1-phosphate aldolase / sphinganine-1-phosphate aldolase activity / luteinization / sphingolipid catabolic process / ceramide metabolic process / sphingolipid biosynthetic process / Leydig cell differentiation / fibroblast migration / skeletal system morphogenesis ...Sphingolipid metabolism / sphinganine-1-phosphate aldolase / sphinganine-1-phosphate aldolase activity / luteinization / sphingolipid catabolic process / ceramide metabolic process / sphingolipid biosynthetic process / Leydig cell differentiation / fibroblast migration / skeletal system morphogenesis / face morphogenesis / estrogen metabolic process / roof of mouth development / platelet-derived growth factor receptor signaling pathway / hemopoiesis / androgen metabolic process / regulation of multicellular organism growth / vasculogenesis / post-embryonic development / fatty acid metabolic process / kidney development / apoptotic signaling pathway / pyridoxal phosphate binding / spermatogenesis / endoplasmic reticulum membrane / endoplasmic reticulum
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
ACETATE ION / Sphingosine-1-phosphate lyase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsGiardina, G. / Catalano, F. / Pampalone, G. / Cellini, B.
Funding support Italy, 3items
OrganizationGrant numberCountry
Other governmentRP11916B407928AA Italy
Other governmentRM12117A5BDD4AEC Italy
Other privateFFC#16/2020 Italy
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
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,2996
Polymers109,9972
Non-polymers3024
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-102 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.160, 127.410, 66.950
Angle α, β, γ (deg.)90.000, 104.850, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Sphingosine-1-phosphate lyase 1 / S1PL / SP-lyase 1 / SPL 1 / hSPL / Sphingosine-1-phosphate aldolase


Mass: 54998.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed as a deletion mutant of the first 81 residues - Delta81
Source: (gene. exp.) Homo sapiens (human) / Gene: SGPL1, KIAA1252 / Plasmid: pET28-b
Details (production host): co transformed with pGRO7 plasmid from Takara containing GroEL and GroES chaperonins
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: O95470, sphinganine-1-phosphate aldolase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.63 % / Description: Platelets
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: hSPL 108uM in Tris-HCl 20 mM pH 8.0 NaCl 150 mM DTT 1mM Glycerol 5% Precipitant: (Hit G4 of Molecular Dimension screen Morpheus) 0.02M Sodium formate; 0.02M Ammonium ...Details: Protein solution: hSPL 108uM in Tris-HCl 20 mM pH 8.0 NaCl 150 mM DTT 1mM Glycerol 5% Precipitant: (Hit G4 of Molecular Dimension screen Morpheus) 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate; Imidazole 0.05M; MES monohydrate (acid) 0.05M; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 mixing volumes: 0.3 + 0.3 uL

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2022
Details: Cilindrical Mirror with 50 nm Pt-coating Radius (calculated) = 14 km Distance from source = 21200 mm Incidence angle = 3 mrad Active length = 1200 mm
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→57.76 Å / Num. obs: 47604 / % possible obs: 92.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.8
Reflection shellResolution: 1.84→2.09 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2380 / CC1/2: 0.421 / % possible all: 67.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.532
Highest resolutionLowest resolution
Rotation57.7 Å2.31 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q6R

4q6r


Resolution: 1.84→57.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.1816 / WRfactor Rwork: 0.16 / FOM work R set: 0.8278 / SU B: 4.289 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2877 / SU Rfree: 0.1937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 2499 5.2 %RANDOM
Rwork0.1907 ---
obs0.192 45105 57.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.44 Å2 / Biso mean: 21.609 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.84→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 28 319 7205
Biso mean--23.87 27.82 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127079
X-RAY DIFFRACTIONr_bond_other_d0.0110.0166472
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6429599
X-RAY DIFFRACTIONr_angle_other_deg0.5181.55615042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.549536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.486101125
X-RAY DIFFRACTIONr_chiral_restr0.0660.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021439
LS refinement shellResolution: 1.84→1.886 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.421 5 -
Rwork0.282 149 -
obs--2.52 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more