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- PDB-7p4o: Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC -

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Basic information

Entry
Database: PDB / ID: 7p4o
TitleCrystal structure of Autotaxin and 9(R)-delta6a,10a-THC
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 2
KeywordsHYDROLASE / 9(R)-delta6a / 10a-THC / inhibitor
Function / homology
Function and homology information


response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell-matrix adhesion / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / cellular response to cadmium ion / cell chemotaxis / cellular response to estradiol stimulus / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / calcium ion binding / positive regulation of cell population proliferation / extracellular space / zinc ion binding
Similarity search - Function
Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A ...Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
7alpha-hydroxycholesterol / Chem-5K9 / IODIDE ION / THIOCYANATE ION / Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsEymery, M.C. / McCarthy, A.A. / Hausmann, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
Citation
Journal: Life Sci Alliance / Year: 2023
Title: Linking medicinal cannabis to autotaxin-lysophosphatidic acid signaling.
Authors: Eymery, M.C. / McCarthy, A.A. / Hausmann, J.
#1: Journal: Acta Crystallogr. D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine
Authors: Afonine, P.V.
History
DepositionJul 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,17523
Polymers95,0381
Non-polymers3,13822
Water8,305461
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-54 kcal/mol
Surface area31720 Å2
Unit cell
Length a, b, c (Å)53.841, 62.361, 64.356
Angle α, β, γ (deg.)103.698, 98.371, 93.439
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD


Mass: 95037.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 9(R)-delta6a,10a-THC / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Production host: Homo sapiens (human)
References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 482 molecules

#3: Chemical ChemComp-5JK / 7alpha-hydroxycholesterol / (3beta,7alpha,9beta,14beta)-cholest-5-ene-3,7-diol / 7α-Hydroxycholesterol


Mass: 402.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H46O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-5K9 / (9~{R},10~{a}~{S})-6,6,9-trimethyl-3-pentyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol


Mass: 316.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop
Details: 18-22% (m/v) PEG3350, 0.1-0.3 M NH4I and 0.3 M NaSCN rATX: 3mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.69→60.29 Å / Num. obs: 85240 / % possible obs: 94.81 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.89 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.1146 / Net I/σ(I): 7.53
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 1.037 / Num. unique obs: 8434 / CC1/2: 0.548 / % possible all: 94.23

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
autoPROCdata processing
Cootmodel building
PHENIXmodel building
pointlessdata scaling
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XR9

2xr9


Resolution: 1.69→60.29 Å / SU ML: 0.1476 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.9811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2058 2003 2.35 %
Rwork0.1711 83237 -
obs0.1719 85240 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.89 Å2
Refinement stepCycle: LAST / Resolution: 1.69→60.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6244 0 113 461 6818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756523
X-RAY DIFFRACTIONf_angle_d0.89628853
X-RAY DIFFRACTIONf_chiral_restr0.0566934
X-RAY DIFFRACTIONf_plane_restr0.00581135
X-RAY DIFFRACTIONf_dihedral_angle_d9.2514900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.24271330.21775932X-RAY DIFFRACTION94.22
1.73-1.780.24591440.20655904X-RAY DIFFRACTION94.19
1.78-1.830.24151400.19415951X-RAY DIFFRACTION95.34
1.83-1.890.21531480.18646028X-RAY DIFFRACTION95.74
1.89-1.960.23111520.18756011X-RAY DIFFRACTION95.98
1.96-2.030.21731380.17926037X-RAY DIFFRACTION96.39
2.03-2.130.22791560.18146040X-RAY DIFFRACTION96.27
2.13-2.240.20021410.17456057X-RAY DIFFRACTION96.53
2.24-2.380.23131430.17976047X-RAY DIFFRACTION96.51
2.38-2.560.22921520.18766074X-RAY DIFFRACTION96.51
2.56-2.820.20371380.18485946X-RAY DIFFRACTION95.08
2.82-3.230.21111390.17955781X-RAY DIFFRACTION92.08
3.23-4.070.20611390.14765714X-RAY DIFFRACTION91.27
4.07-60.290.1671400.15325715X-RAY DIFFRACTION91.14
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)
10.6804616634750.04402034351290.2099963193091.477894890360.3529289636581.099747861610.00362025171594-0.107225804114-0.01187338153070.2725471864750.0506268869212-0.07073557701140.02540042910080.00847786031244-0.04318774960190.1583982962780.01494491557830.00315402879570.1553320704870.01666562897650.144933966332-0.24292617935625.32451833482.29899900037
20.854198877598-0.06477565574120.4476810903160.583173104947-0.1162087875360.728546139474-0.1842476910630.2648249197280.226551481358-0.3195762420630.05638552236410.142173132432-0.329494061880.008368996614710.1350242123860.361204108134-0.0299513652716-0.02521646580360.2742130450890.06233118561650.237913973678-17.525717249134.7443544919-31.3215662748
31.173223087940.005190348749380.3692850541021.428934202680.2711249181791.219196752760.00181393951070.19252257318-0.0322773141946-0.1651208379970.008350140248610.0781911537394-0.001817602997290.0191104605062-0.0106901367010.140804459843-0.0216435715314-0.004469913766440.1851767915180.008332551519150.128812729262-22.912452753121.159785172-31.414058514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 516 )
2X-RAY DIFFRACTION2chain 'A' and (resid 517 through 597 )
3X-RAY DIFFRACTION3chain 'A' and (resid 598 through 858 )

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