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- PDB-6g4g: Full length ectodomain of ectonucleotide phosphodiesterase/pyroph... -

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Basic information

Entry
Database: PDB / ID: 6g4g
TitleFull length ectodomain of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) including the SMB domains but with a partially disordered active site structure
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 3
KeywordsHYDROLASE / enzyme / ectonucleotide phosphodiesterase/pyrophosphatase / complex / zinc / SMB / PDE
Function / homology
Function and homology information


basophil activation involved in immune response / negative regulation of mast cell activation involved in immune response / phosphodiesterase I / dinucleotide phosphatase activity / nucleoside triphosphate catabolic process / nucleotide diphosphatase / regulation of smooth muscle cell differentiation / negative regulation of mast cell proliferation / nucleoside triphosphate diphosphatase activity / pyrimidine nucleotide metabolic process ...basophil activation involved in immune response / negative regulation of mast cell activation involved in immune response / phosphodiesterase I / dinucleotide phosphatase activity / nucleoside triphosphate catabolic process / nucleotide diphosphatase / regulation of smooth muscle cell differentiation / negative regulation of mast cell proliferation / nucleoside triphosphate diphosphatase activity / pyrimidine nucleotide metabolic process / phosphate ion homeostasis / phosphodiesterase I activity / phosphate-containing compound metabolic process / ATP metabolic process / negative regulation of inflammatory response / nucleic acid binding / apical plasma membrane / external side of plasma membrane / calcium ion binding / perinuclear region of cytoplasm / cell surface / zinc ion binding / extracellular region
Similarity search - Function
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 ...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 superfamily / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDohler, C. / Zebisch, M. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation477/13-2 Germany
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain.
Authors: Dohler, C. / Zebisch, M. / Krinke, D. / Robitzki, A. / Strater, N.
History
DepositionMar 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
C: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
D: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,20423
Polymers382,3034
Non-polymers4,90119
Water0
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1287
Polymers95,5761
Non-polymers1,5536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4835
Polymers95,5761
Non-polymers9074
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6865
Polymers95,5761
Non-polymers1,1104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9076
Polymers95,5761
Non-polymers1,3315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.360, 116.300, 124.160
Angle α, β, γ (deg.)86.77, 87.76, 88.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 / E-NPP 3 / B10 / Phosphodiesterase I beta / PD-Ibeta / Phosphodiesterase I/nucleotide ...E-NPP 3 / B10 / Phosphodiesterase I beta / PD-Ibeta / Phosphodiesterase I/nucleotide pyrophosphatase 3 / RB13-6 antigen


Mass: 95575.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp3, Pdnp3 / Plasmid: pHLsec / Cell line (production host): HEK293S GnTI- / Organ (production host): kindney / Production host: Homo sapiens (human)
References: UniProt: P97675, phosphodiesterase I, nucleotide diphosphatase
#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.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.92 Å3/Da / Density % sol: 57.8 % / Description: irregular shape
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M tri-ammonium citrate pH 7.0, 20% (w/v) PEG 3350, grown after 3 month

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Sep 12, 2012 / Details: 2 MIRRORS AND A DOUBLE-CRYSTAL MONOCHROMATOR
RadiationMonochromator: KMC-1, Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→47.22 Å / Num. obs: 68486 / % possible obs: 65.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 67.42 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.239
Reflection shellResolution: 2.8→3.04 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 1.268 / % possible all: 14.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
DIALSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XR9

2xr9


Resolution: 2.8→47.22 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.878 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.436
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3360 4.91 %RANDOM
Rwork0.196 ---
obs0.198 68479 65.3 %-
Displacement parametersBiso mean: 78.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.5791 Å21.6881 Å20.7407 Å2
2---5.3613 Å20.6213 Å2
3---7.9404 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24474 0 312 0 24786
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125542HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1634768HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8684SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes629HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3649HARMONIC5
X-RAY DIFFRACTIONt_it25542HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion21.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3287SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28770SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 -5.68 %
Rwork0.28 730 -
all0.282 774 -
obs--9.97 %
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)
10.96070.0586-0.01940.8439-0.39693.7827-0.07840.2458-0.1676-0.26340.0580.09730.0032-0.7150.0204-0.09950.06510.10090.1378-0.00850.1962-11.0314.936139.9113
20.41830.0251-1.20190.4982-0.48064.37090.17270.17550.2121-0.03380.15920.1160.5803-0.9432-0.33190.1778-0.0471-0.03970.16390.29150.2816-4.965189.4724121.2906
31.1915-0.55640.4011.13610.02932.8526-0.3145-0.17980.37680.09620.1354-0.36670.11250.31560.17920.31620.05-0.0433-0.14850.02010.229324.92571.653460.5555
40.70440.2469-0.31140.67230.38952.7217-0.07150.1089-0.14780.12820.1083-0.2187-0.28390.1927-0.03690.0960.07290.04380.07680.00620.20524.286430.670196.2645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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