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- PDB-6f33: Crystal structure of ectonucleotide phosphodiesterase/pyrophospha... -

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Basic information

Entry
Database: PDB / ID: 6f33
TitleCrystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex with AMPNPP
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 3
KeywordsHYDROLASE / enzyme / ectonucleotide phosphodiesterase/pyrophosphatase / complex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


GTP diphosphatase activity / bis(5'-adenosyl)-triphosphatase activity / negative regulation of mast cell activation involved in immune response / basophil activation involved in immune response / UTP diphosphatase activity / dinucleotide phosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleoside triphosphate catabolic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / phosphodiesterase I ...GTP diphosphatase activity / bis(5'-adenosyl)-triphosphatase activity / negative regulation of mast cell activation involved in immune response / basophil activation involved in immune response / UTP diphosphatase activity / dinucleotide phosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleoside triphosphate catabolic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / phosphodiesterase I / nucleotide diphosphatase / negative regulation of mast cell proliferation / regulation of smooth muscle cell differentiation / nucleoside triphosphate diphosphatase activity / pyrimidine nucleotide metabolic process / ATP diphosphatase activity / phosphate ion homeostasis / phosphate-containing compound metabolic process / phosphodiesterase I activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / 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 / extracellular region / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Gyrase A; domain 2 - #180 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 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 ...Gyrase A; domain 2 - #180 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 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 / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZAN / Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)174,87918
Polymers170,7392
Non-polymers4,14016
Water00
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5419
Polymers85,3691
Non-polymers2,1728
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)87,3389
Polymers85,3691
Non-polymers1,9688
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.492, 126.935, 112.245
Angle α, β, γ (deg.)90.00, 96.75, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp3, Pdnp3 / Cell line (production host): HEK293S Gnt- / Production host: Homo sapiens (human)
References: UniProt: P97675, phosphodiesterase I, nucleotide diphosphatase

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Sugars , 2 types, 8 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.: 5
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
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 3 types, 8 molecules

#3: Chemical ChemComp-ZAN / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 60.14 %
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: 2.9→47.26 Å / Num. obs: 45100 / % possible obs: 98.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 73.53 Å2 / Net I/σ(I): 2.4
Reflection shellResolution: 2.9→3 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: 3→47.26 Å / Cor.coef. Fo:Fc: 0.789 / Cor.coef. Fo:Fc free: 0.771 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.419
RfactorNum. reflection% reflectionSelection details
Rfree0.268 809 2 %RANDOM
Rwork0.245 ---
obs0.246 40503 97.4 %-
Displacement parametersBiso mean: 76.71 Å2
Baniso -1Baniso -2Baniso -3
1-16.2843 Å20 Å211.8045 Å2
2--10.4863 Å20 Å2
3----26.7706 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: 1 / Resolution: 3→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11581 0 250 0 11831
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712202HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8816652HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4125SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1763HARMONIC5
X-RAY DIFFRACTIONt_it12202HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.71
X-RAY DIFFRACTIONt_other_torsion20.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1563SEMIHARMONIC5
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_contact13556SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 -1.57 %
Rwork0.245 2950 -
all0.245 2997 -
obs--98.01 %
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)
12.64920.44440.54751.8631-0.14951.28540.2095-0.11690.0101-0.31550.0711-0.0263-0.1055-0.0316-0.28060.1821-0.1057-0.0945-0.09140.0683-0.3331-11.6610.505233.1784
20.82770.66980.22852.013-0.79352.2320.02460.0205-0.22960.0335-0.04360.1616-0.0396-0.02840.019-0.1471-0.1648-0.2054-0.21070.09920.2617-36.5415-15.87740.4543
31.35490.01171.32330.8880.64041.0904-0.03230.0264-0.04770.53370.2662-0.11830.06860.4503-0.23390.21990.1343-0.090.0428-0.1281-0.332614.2054-13.21290.6245
41.53951.20960.63612.938-0.2182.861-0.03750.1980.11850.06190.27610.5554-0.10940.2845-0.2386-0.20320.00850.0145-0.05780.06290.0508-11.5612-16.4431-25.8554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - A|550}
2X-RAY DIFFRACTION2{A|551 - A|1000 }
3X-RAY DIFFRACTION3{B|1 - B|550}
4X-RAY DIFFRACTION4{B|551 - B|1000 }

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