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- PDB-6wg5: Human ectonucleoside triphosphate diphosphohydrolase 4 (ENTPD4, N... -

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Basic information

Entry
Database: PDB / ID: 6wg5
TitleHuman ectonucleoside triphosphate diphosphohydrolase 4 (ENTPD4, NTPDase 4)
ComponentsEctonucleoside triphosphate diphosphohydrolase 4
KeywordsHYDROLASE / nucleotide metabolism / glycosylation / ASKHA superfamily
Function / homology
Function and homology information


guanosine-diphosphatase / UDP catabolic process / CTP metabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleobase-containing small molecule catabolic process / : / GDP catabolic process / CDP phosphatase activity / nucleoside diphosphate phosphatase / nucleoside diphosphate catabolic process ...guanosine-diphosphatase / UDP catabolic process / CTP metabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleobase-containing small molecule catabolic process / : / GDP catabolic process / CDP phosphatase activity / nucleoside diphosphate phosphatase / nucleoside diphosphate catabolic process / : / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / CTPase activity / GDP phosphatase activity / autophagosome membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / cytoplasmic vesicle / lysosomal membrane / Golgi membrane / GTPase activity / Golgi apparatus / membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family
Similarity search - Domain/homology
Ectonucleoside triphosphate diphosphohydrolase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGorelik, A. / Labriola, J.M. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Protein Sci. / Year: 2020
Title: Crystal structure of the nucleotide-metabolizing enzyme NTPDase4.
Authors: Gorelik, A. / Labriola, J.M. / Illes, K. / Nagar, B.
History
DepositionApr 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Ectonucleoside triphosphate diphosphohydrolase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3422
Polymers58,9171
Non-polymers4241
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.378, 101.820, 129.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ectonucleoside triphosphate diphosphohydrolase 4 / NTPDase 4 / Lysosomal apyrase-like protein of 70 kDa / Uridine-diphosphatase / UDPase


Mass: 58917.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENTPD4, KIAA0392, LALP70, LYSAL1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y227, nucleoside diphosphate phosphatase
#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.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Na/K tartrate, 20% PEG 3350, cryo-protected with 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22486 / % possible obs: 95 % / Redundancy: 7.2 % / CC1/2: 1 / Rrim(I) all: 0.108 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.9 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1864 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZX3

3zx3


Resolution: 2.6→49.322 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.99
RfactorNum. reflection% reflection
Rfree0.2136 1864 8.29 %
Rwork0.1742 --
obs0.1774 22484 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.24 Å2 / Biso mean: 56.9656 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 2.6→49.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 55 204 4236
Biso mean--85.01 45.26 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024131
X-RAY DIFFRACTIONf_angle_d0.5215604
X-RAY DIFFRACTIONf_chiral_restr0.041601
X-RAY DIFFRACTIONf_plane_restr0.003731
X-RAY DIFFRACTIONf_dihedral_angle_d16.2932467
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6001-2.67040.2821970.2488107566
2.6704-2.7490.25441170.2295129080
2.749-2.83770.26021350.2208149390
2.8377-2.93910.22451460.2104161899
2.9391-3.05680.24611490.2031649100
3.0568-3.19590.24811480.19451641100
3.1959-3.36430.21941500.18631659100
3.3643-3.57510.24261500.16771651100
3.5751-3.8510.19081500.1551665100
3.851-4.23840.17061520.14241676100
4.2384-4.85120.14831530.13171696100
4.8512-6.11020.22041540.161703100
6.1102-49.3220.24081630.19641804100
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)
12.66460.85091.20122.39-0.9512.0518-0.1519-0.0685-0.10750.0679-0.2004-0.48370.06220.37740.26110.26140.01850.06730.46720.06930.38554.942616.488522.5933
22.3808-0.26310.8062.7323-0.15912.42220.1529-0.0386-0.9668-0.2999-0.1635-0.40480.9980.3906-0.05920.68350.15560.11150.41480.16390.77062.1096-4.428722.91
32.720.37390.24041.24270.09442.8073-0.09130.08650.201-0.06770.00040.0596-0.08160.12580.12650.1683-0.0070.05150.23320.04890.2135-8.800519.933717.4912
40.51620.57310.84422.07210.37281.6032-0.1749-0.13720.02020.27940.06010.3710.0463-0.3088-0.00650.23110.00460.07520.2752-0.01850.2793-18.112118.818314.3929
51.05370.07710.1630.9663-0.04520.7408-0.0141-0.0129-0.10690.13590.05420.20240.2344-0.25480.13040.2147-0.03860.10890.29010.02260.2439-19.98867.92198.8077
61.82710.8530.38231.62140.56821.5005-0.15080.3207-0.4347-0.42560.046-0.0519-0.0714-0.05920.06350.2513-0.0573-0.01710.3586-0.07950.2147-15.46861.4578-18.9299
72.22060.7255-1.01041.69430.50983.26710.0051-0.0110.0641-0.1190.043-0.1444-0.28860.1204-0.04660.1952-0.01070.010.12930.0070.1568-6.954615.6206-5.8872
80.57560.6228-0.61132.2634-2.47322.71470.2127-0.14790.14690.6372-0.051-0.2741-0.4650.5520.30080.44290.01470.06310.32890.09440.3722-7.678812.142638.7184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 64 through 127 )A64 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 218 )A128 - 218
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 246 )A219 - 246
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 282 )A247 - 282
5X-RAY DIFFRACTION5chain 'A' and (resid 283 through 346 )A283 - 346
6X-RAY DIFFRACTION6chain 'A' and (resid 347 through 413 )A347 - 413
7X-RAY DIFFRACTION7chain 'A' and (resid 414 through 525 )A414 - 525
8X-RAY DIFFRACTION8chain 'A' and (resid 526 through 555 )A526 - 555

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