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- PDB-2xr9: Crystal structure of Autotaxin (ENPP2) -

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Basic information

Entry
Database: PDB / ID: 2xr9
TitleCrystal structure of Autotaxin (ENPP2)
ComponentsECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
KeywordsHYDROLASE / LYSOPHOSPHATIDYLCHOLINE / SOMATOMEDIN / INFLAMMATION / METASTASIS / NEUROPATHIC PAIN / VASCULAR DEVELOPMENT / NEURAL DEVELOPMENT
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
IODIDE ION / PHOSPHATE ION / THIOCYANATE ION / Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsKamtekar, S. / Hausmann, J. / Day, J.E. / Christodoulou, E. / Perrakis, A.
Citation
Journal: Nat. Struct. Mol. Biol. / Year: 2011
Title: Structural basis of substrate discrimination and integrin binding by autotaxin.
Authors: Hausmann, J. / Kamtekar, S. / Christodoulou, E. / Day, J.E. / Wu, T. / Fulkerson, Z. / Albers, H.M. / van Meeteren, L.A. / Houben, A.J. / van Zeijl, L. / Jansen, S. / Andries, M. / Hall, T. ...Authors: Hausmann, J. / Kamtekar, S. / Christodoulou, E. / Day, J.E. / Wu, T. / Fulkerson, Z. / Albers, H.M. / van Meeteren, L.A. / Houben, A.J. / van Zeijl, L. / Jansen, S. / Andries, M. / Hall, T. / Pegg, L.E. / Benson, T.E. / Kasiem, M. / Harlos, K. / Kooi, C.W. / Smyth, S.S. / Ovaa, H. / Bollen, M. / Morris, A.J. / Moolenaar, W.H. / Perrakis, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Mammalian Cell Expression, Purification, Crystallization and Microcrystal Data Collection of Autotaxin/Enpp2, a Secreted Mammalian Glycoprotein.
Authors: Hausmann, J. / Christodoulou, E. / Kasiem, M. / De Marco, V. / van Meeteren, L.A. / Moolenaar, W.H. / Axford, D. / Owen, R.L. / Evans, G. / Perrakis, A.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Rat Autotaxin.
Authors: Day, J.E. / Hall, T. / Pegg, L.E. / Benson, T.E. / Hausmann, J. / Kamtekar, S.
History
DepositionSep 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 2.1Dec 20, 2023Group: 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

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)99,68538
Polymers95,0471
Non-polymers4,63837
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.808, 63.289, 70.471
Angle α, β, γ (deg.)98.78, 106.22, 99.77
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 / AUTOTAXIN ENPP2 / EXTRACELLULAR LYSOPHOSPHOLIPASE D / LYSOPLD


Mass: 95046.664 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / Variant (production host): FLIPIN
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 , 6 types, 368 molecules

#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 410 TO ALA
Nonpolymer detailsPHOSPHATE ION (PO4): PRESENT IN CRYSTALLIZATION BUFFER AND BOUND NEARBY CATALYTIC SITE OF THE ...PHOSPHATE ION (PO4): PRESENT IN CRYSTALLIZATION BUFFER AND BOUND NEARBY CATALYTIC SITE OF THE PHOSPHODIESTERASE IODINE ION (IOD): PRESENT IN CRYSTALLIZATION BUFFER AND USED FOR SAD PHASING, MODELED TO FOURIER ANOMALOUS SIGNAL OF ABOVE 4.5 SIGMA CALCIUM ION (CA): INFERRED FROM BINDING TO EF-HAND LIKE MOTIF AND CHEMICAL COORDINATION ZINC ION (ZN): PRESUMED FROM THE CATALYTIC MECHANISM AND CONFIRMED BY ANOMALOUS SIGNAL MANNOSE (MAN): GLYCOSYLATION THIOCYANATE (SCN): PRESENT IN CRYSTALLIZATION BUFFER N-ACETYL-GLUCOSAMINE (NAG): GLYCOSYLATION
Sequence detailsTHE SEQUENCE IS ISOFORM 2 OF THE PROTEIN

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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: 2.2 Å3/Da / Density % sol: 45 %
Description: MOLECULAR REPLACEMENT USED ONLY FOR FINDING SITES THROUGH AUTOMATED PROCEDURES IN PHASER.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.283
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 52153 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.49 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2GSN

2gsn


Resolution: 2.05→19.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.518 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22053 2588 5 %RANDOM
Rwork0.17264 ---
obs0.175 49561 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0.47 Å20.98 Å2
2--0.01 Å2-0.12 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 87 332 6745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226581
X-RAY DIFFRACTIONr_bond_other_d0.0010.024599
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9638930
X-RAY DIFFRACTIONr_angle_other_deg0.983.00511085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36523.143315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.809151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7891549
X-RAY DIFFRACTIONr_chiral_restr0.1010.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021389
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7931.53927
X-RAY DIFFRACTIONr_mcbond_other0.2161.51561
X-RAY DIFFRACTIONr_mcangle_it1.43826377
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27532654
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5274.52552
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 173 -
Rwork0.251 3483 -
obs--93.15 %
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)
13.9055-1.74093.70193.9435-3.73267.799-0.15360.31980.3132-0.1051-0.123-0.8648-0.39020.81340.27660.3608-0.11670.16720.3112-0.05170.336119.58677.35314.703
21.4004-0.1951-0.03472.0654-0.71362.70990.05120.12180.2177-0.10250.0547-0.0357-0.366-0.0134-0.10590.08290.0080.03190.04880.02160.04243.3861.79623.825
31.15980.3467-0.78161.461-0.69983.20870.1824-0.02170.15330.1376-0.0425-0.0125-0.43310.1117-0.13990.07520.00250.02790.0351-0.00130.02420.8761.80633.193
42.8941.02491.00264.33191.1050.5399-0.20160.1668-0.9105-0.11570.39720.17170.09360.0072-0.19550.675-0.34630.12520.3342-0.07690.363-20.42521.51633.011
52.14550.62460.18671.7720.12052.7290.0468-0.0697-0.26170.2193-0.07740.08710.4241-0.26120.03060.0927-0.04280.02240.0356-0.00180.0495-17.72934.29141.643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 133
2X-RAY DIFFRACTION2A134 - 268
3X-RAY DIFFRACTION3A269 - 535
4X-RAY DIFFRACTION4A536 - 601
5X-RAY DIFFRACTION5A602 - 859

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