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- PDB-3cj1: Structure of Rattus norvegicus NTPDase2 -

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Basic information

Entry
Database: PDB / ID: 3cj1
TitleStructure of Rattus norvegicus NTPDase2
ComponentsEctonucleoside triphosphate diphosphohydrolase 2
KeywordsHYDROLASE / alpha/beta protein / Actin-like fold / Alternative splicing / Calcium / Glycoprotein / Magnesium / Membrane / Transmembrane
Function / homology
Function and homology information


purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane ...purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane / cellular response to interleukin-6 / basement membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribonucleoside triphosphate phosphatase activity / platelet activation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / cell body / G protein-coupled receptor signaling pathway / cell surface / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / Exopolyphosphatase. Domain 2 / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ectonucleoside triphosphate diphosphohydrolase 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsZebisch, M. / Strater, N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling
Authors: Zebisch, M. / Strater, N.
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ectonucleoside triphosphate diphosphohydrolase 2


Theoretical massNumber of molelcules
Total (without water)50,6121
Polymers50,6121
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.346, 69.029, 164.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ectonucleoside triphosphate diphosphohydrolase 2 / NTPDase 2 / Ecto-ATPase / CD39 antigen-like 1


Mass: 50611.949 Da / Num. of mol.: 1
Fragment: Ectodomain, Extracellular domain, UNP residues 29-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Entpd2 / Plasmid: pET45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O35795, apyrase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ENTP2_RAT.

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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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100mM NaHEPES, 2% PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.947 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 1.7→34.48 Å / Num. all: 52974 / Num. obs: 52974 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→33.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.473 / SU ML: 0.06 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20385 1086 2.1 %RANDOM
Rwork0.17507 ---
obs0.17567 51660 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.785 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 0 388 3682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9474600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89522.961152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.081525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022600
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21548
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22346
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0961.52152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56523370
X-RAY DIFFRACTIONr_scbond_it2.67131425
X-RAY DIFFRACTIONr_scangle_it4.054.51227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 75 -
Rwork0.241 3777 -
obs--99.69 %

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