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- PDB-6f2y: Crystal structure of ectonucleotide phosphodiesterase/pyrophospha... -

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Basic information

Entry
Database: PDB / ID: 6f2y
TitleCrystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex with Ap4A
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 3
KeywordsHYDROLASE / enzyme / ectonucleotide phosphodiesterase/pyrophosphatase / CYTOSOLIC PROTEIN
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 / 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
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDohler, C. / Zebisch, M. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation477/13-2 Germany
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3).
Authors: Dohler, C. / Zebisch, M. / Strater, N.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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.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 / _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_type.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)176,58622
Polymers170,7392
Non-polymers5,84720
Water7,764431
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,09210
Polymers85,3691
Non-polymers2,7239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,49412
Polymers85,3691
Non-polymers3,12411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.940, 126.850, 114.480
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 85369.352 Da / Num. of mol.: 2 / Mutation: T206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp3, Pdnp3 / Cell line (production host): HEK293S GntI- / Production host: Homo sapiens (human)
References: UniProt: P97675, phosphodiesterase I, nucleotide diphosphatase

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Sugars , 3 types, 12 molecules

#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.: 4
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: 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
#7: 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.: 7
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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Non-polymers , 4 types, 439 molecules

#4: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M KCl, 0.1 M MgAcetate, 0.05 NaCacodylate pH 6.0, 10.2% PEG8000, 1 mM CaCl2, 0.1 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→48.24 Å / Num. obs: 81943 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 57.22 Å2 / Rpim(I) all: 0.122 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.45 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimless1.6.18data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XR9

2xr9


Resolution: 2.4→48.24 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.921 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.294 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.203
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1615 1.97 %RANDOM
Rwork0.204 ---
obs0.204 81830 98.7 %-
Displacement parametersBiso mean: 56.65 Å2
Baniso -1Baniso -2Baniso -3
1-5.0259 Å20 Å26.277 Å2
2---3.5556 Å20 Å2
3----1.4703 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.4→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11584 0 361 431 12376
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712327HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9216841HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4190SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1805HARMONIC5
X-RAY DIFFRACTIONt_it12327HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion17.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1605SEMIHARMONIC5
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_contact14274SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 107 1.76 %
Rwork0.226 5967 -
all0.226 6074 -
obs--99.7 %
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)
11.51750.2735-0.28321.0491-0.15971.11690.08540.0020.07110.0148-0.0171-0.0056-0.0963-0.0239-0.0683-0.0829-0.0003-0.027-0.05720.0095-0.1877-12.15110.549433.6906
21.24880.5343-0.40291.4203-0.39820.65960.10440.059-0.33870.0344-0.03820.11150.1101-0.2255-0.0662-0.179-0.0888-0.07560.04530.0623-0.0481-37.1775-15.83641.3861
31.04720.25640.72221.28770.70521.70230.05960.0101-0.03320.1940.1453-0.12420.15450.3183-0.205-0.15250.0384-0.05540-0.0458-0.190513.8515-13.261.021
41.38930.50010.72481.55930.37852.1266-0.01990.10710.0123-0.14770.06360.2954-0.0932-0.0673-0.0437-0.12970.0272-0.0739-0.0515-0.0157-0.1215-11.2232-16.4436-26.4154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|140 - A|550}
2X-RAY DIFFRACTION2{A|551 - A|871 }
3X-RAY DIFFRACTION3{B|140 - B|550}
4X-RAY DIFFRACTION4{B|551 - B|871 }

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