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- PDB-6fiw: Human cytosolic 5'-nucleotidase II co-crystallized with 10mM Sodi... -

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Basic information

Entry
Database: PDB / ID: 6fiw
TitleHuman cytosolic 5'-nucleotidase II co-crystallized with 10mM Sodium ((4-(3'-((7H-purin-6-yl)carbamoyl)-[1,1'-biphenyl]-3-yl)-1H-imidazol-1-yl) methyl) phosphonate
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE
Function / homology
Function and homology information


nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP catabolic process / IMP metabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsAghajari, N. / Preeti, P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research Agency2011-SIMI7 France
INCa2010-200 France
CitationJournal: Eur J Med Chem / Year: 2019
Title: Lead optimization and biological evaluation of fragment-based cN-II inhibitors.
Authors: Guillon, R. / Rahimova, R. / Egron, D. / Rouanet, S. / Dumontet, C. / Aghajari, N. / Jordheim, L.P. / Chaloin, L. / Peyrottes, S.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5487
Polymers62,0561
Non-polymers4936
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-44 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.070, 128.350, 129.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cytosolic purine 5'-nucleotidase / Cytosolic 5'-nucleotidase II


Mass: 62055.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: P28A-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: MGSO4, TRIS AND LIGAND, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. obs: 38716 / % possible obs: 99.4 % / Redundancy: 4 % / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2JC

Resolution: 2.2→48.854 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.64
RfactorNum. reflection% reflection
Rfree0.2184 1936 5 %
Rwork0.182 --
obs0.1838 38702 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 29 137 4063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084042
X-RAY DIFFRACTIONf_angle_d0.8935456
X-RAY DIFFRACTIONf_dihedral_angle_d5.1843321
X-RAY DIFFRACTIONf_chiral_restr0.051577
X-RAY DIFFRACTIONf_plane_restr0.005690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.33341370.29582615X-RAY DIFFRACTION100
2.255-2.3160.32441380.26712610X-RAY DIFFRACTION100
2.316-2.38420.31981360.24862576X-RAY DIFFRACTION99
2.3842-2.46110.27841350.23792580X-RAY DIFFRACTION99
2.4611-2.54910.29081390.23182630X-RAY DIFFRACTION100
2.5491-2.65110.28391360.20122584X-RAY DIFFRACTION99
2.6511-2.77180.24111380.20032619X-RAY DIFFRACTION100
2.7718-2.91790.22671380.19512613X-RAY DIFFRACTION99
2.9179-3.10070.24231370.19782611X-RAY DIFFRACTION99
3.1007-3.340.2181370.18542610X-RAY DIFFRACTION100
3.34-3.6760.20171400.16382644X-RAY DIFFRACTION99
3.676-4.20770.16221380.15112638X-RAY DIFFRACTION99
4.2077-5.30030.18011410.15012675X-RAY DIFFRACTION99
5.3003-48.86610.2221460.18182761X-RAY DIFFRACTION99

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