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- PDB-5dlt: Crystal structure of Autotaxin (ENPP2) with 7-alpha-hydroxycholesterol -

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Basic information

Entry
Database: PDB / ID: 5dlt
TitleCrystal structure of Autotaxin (ENPP2) with 7-alpha-hydroxycholesterol
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 2
KeywordsHYDROLASE / Autotaxin / ENPP2 / LPA / steroids / bile salts
Function / homology
Function and homology information


response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / positive regulation of lamellipodium morphogenesis / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / negative regulation of cell-matrix adhesion / positive regulation of oligodendrocyte differentiation / 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
Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / 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. ...Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / 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 / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / His-Me finger superfamily / Factor Xa Inhibitor / Alkaline-phosphatase-like, core domain superfamily / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7alpha-hydroxycholesterol / 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: 1.6 Å
AuthorsHausmann, J. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
NWO700.10.354 Netherlands
NWO723.013.003 Netherlands
CitationJournal: Nat Commun / Year: 2016
Title: Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling.
Authors: Keune, W.J. / Hausmann, J. / Bolier, R. / Tolenaars, D. / Kremer, A. / Heidebrecht, T. / Joosten, R.P. / Sunkara, M. / Morris, A.J. / Matas-Rico, E. / Moolenaar, W.H. / Oude Elferink, R.P. / Perrakis, A.
History
DepositionSep 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,87636
Polymers95,1181
Non-polymers3,75935
Water9,476526
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-98 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.671, 63.482, 70.715
Angle α, β, γ (deg.)98.720, 105.800, 99.970
Int Tables number1
Space group name H-MP1

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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: 95117.641 Da / Num. of mol.: 1 / Mutation: N410A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 8 types, 560 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-5JK / 7alpha-hydroxycholesterol / (3beta,7alpha,9beta,14beta)-cholest-5-ene-3,7-diol


Mass: 402.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CNS
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, 0.1M ammonium iodide 0.3M sodium thiocyanate, 23.5mg/ml heparin sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionRedundancy: 2 % / Number: 205646 / Rmerge(I) obs: 0.065 / D res high: 1.6 Å / D res low: 44.02 Å / Num. obs: 105202 / % possible obs: 92.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
1.61.6310.8681.9
8.7644.0210.0292.1
ReflectionResolution: 1.6→44.02 Å / Num. obs: 105202 / % possible obs: 92.1 % / Redundancy: 2 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.061 / Net I/σ(I): 6.7 / Num. measured all: 205646
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.631.90.8680.8972050910.4370.81588.9
8.76-44.022.10.02923.913456430.9960.02792

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Processing

Software
NameVersionClassification
REFMAC5.8.0129refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xr9

2xr9


Resolution: 1.6→44.02 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / Matrix type: sparse / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.166 / SU B: 4.722 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 5262 5 %RANDOM
Rwork0.1713 99938 --
obs0.1725 99938 92.11 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 103.32 Å2 / Biso mean: 28.789 Å2 / Biso min: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0.02 Å20.33 Å2
2--0.21 Å20.1 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.6→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 158 528 7117
Biso mean--38.66 32.56 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226849
X-RAY DIFFRACTIONr_bond_other_d0.0020.026289
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9729284
X-RAY DIFFRACTIONr_angle_other_deg0.955314557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69423.169325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061551
X-RAY DIFFRACTIONr_chiral_restr0.0850.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217571
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021608
X-RAY DIFFRACTIONr_mcbond_it1.4911.8523217
X-RAY DIFFRACTIONr_mcbond_other1.4671.8453207
X-RAY DIFFRACTIONr_mcangle_it2.2952.7554011
X-RAY DIFFRACTIONr_sphericity_bonded11.517513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3533610.3317049X-RAY DIFFRACTION87.434
1.642-1.6870.2993830.3117194X-RAY DIFFRACTION91.731
1.687-1.7350.3013700.2866971X-RAY DIFFRACTION91.637
1.735-1.7890.2623640.266713X-RAY DIFFRACTION91.105
1.789-1.8470.2423210.2356479X-RAY DIFFRACTION90.102
1.847-1.9120.2533530.2146218X-RAY DIFFRACTION89.768
1.912-1.9840.2273250.1935926X-RAY DIFFRACTION89.02
1.984-2.0650.2042930.1695957X-RAY DIFFRACTION93.089
2.065-2.1570.2012950.1645754X-RAY DIFFRACTION93.551
2.157-2.2620.1973090.165558X-RAY DIFFRACTION93.902
2.262-2.3840.1842810.1535201X-RAY DIFFRACTION93.629
2.384-2.5290.1932790.1514944X-RAY DIFFRACTION92.787
2.529-2.7030.1762520.1424718X-RAY DIFFRACTION95.011
2.703-2.9190.1782510.1534408X-RAY DIFFRACTION95.354
2.919-3.1970.1981840.1534039X-RAY DIFFRACTION94.559
3.197-3.5740.1661810.1483650X-RAY DIFFRACTION93.828
3.574-4.1240.1571520.1343237X-RAY DIFFRACTION94.983
4.124-5.0470.1291500.1282713X-RAY DIFFRACTION94.582
5.047-7.1160.2441010.1882081X-RAY DIFFRACTION93.248
7.116-440.164570.2031128X-RAY DIFFRACTION91.577
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)
10.49710.1672-0.30650.5398-0.19010.83750.07020.00060.06380.01080.0014-0.0148-0.13520.0681-0.07160.0443-0.02060.02450.0322-0.00560.017616.78550.533728.9868
20.85880.2684-0.19520.58020.01431.1392-0.0254-0.0012-0.1980.0746-0.04260.03480.3015-0.14970.0680.1079-0.05650.02950.0301-0.01240.066-6.4851-31.782341.8265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 560
2X-RAY DIFFRACTION1A1860 - 1870
3X-RAY DIFFRACTION1A1880 - 1884
4X-RAY DIFFRACTION2A541 - 859
5X-RAY DIFFRACTION2A1871
6X-RAY DIFFRACTION2A1890 - 1894

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