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- PDB-6fis: Human cytosolic 5'-nucleotidase II soaked with 10mM 7-Benzyloxyme... -

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Basic information

Entry
Database: PDB / ID: 6fis
TitleHuman cytosolic 5'-nucleotidase II soaked with 10mM 7-Benzyloxymethyl-7H-adenine
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE
Function / homology
Function and homology information


nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / amide catabolic process ...nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / amide catabolic process / : / dGMP catabolic process / IMP-specific 5'-nucleotidase / : / IMP catabolic process / Ribavirin ADME / IMP metabolic process / Purine catabolism / 5'-nucleotidase / allantoin metabolic process / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Jan 17, 2024Group: 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: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,84110
Polymers62,0561
Non-polymers7859
Water3,945219
1
A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,36240
Polymers248,2234
Non-polymers3,13936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area19670 Å2
ΔGint-452 kcal/mol
Surface area75430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.100, 128.000, 130.700
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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
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: 2.3→50 Å / Num. obs: 34053 / % possible obs: 99.2 % / Redundancy: 4.8 % / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.4 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J2C

2j2c


Resolution: 2.3→49.048 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2019 1701 5 %
Rwork0.1671 --
obs0.1689 34032 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 43 219 4095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073966
X-RAY DIFFRACTIONf_angle_d0.8585356
X-RAY DIFFRACTIONf_dihedral_angle_d6.1922330
X-RAY DIFFRACTIONf_chiral_restr0.05566
X-RAY DIFFRACTIONf_plane_restr0.006674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.36810.31181370.24682625X-RAY DIFFRACTION98
2.3681-2.44450.25661400.21892659X-RAY DIFFRACTION99
2.4445-2.53190.25571410.20742669X-RAY DIFFRACTION99
2.5319-2.63320.2391400.19352668X-RAY DIFFRACTION100
2.6332-2.75310.23961420.19122693X-RAY DIFFRACTION100
2.7531-2.89820.26511410.19572686X-RAY DIFFRACTION100
2.8982-3.07980.27811410.19262672X-RAY DIFFRACTION99
3.0798-3.31750.20851420.17482701X-RAY DIFFRACTION100
3.3175-3.65130.19311430.15122719X-RAY DIFFRACTION99
3.6513-4.17940.14371410.13382678X-RAY DIFFRACTION99
4.1794-5.26460.15291440.13262750X-RAY DIFFRACTION100
5.2646-49.05860.19411490.17632811X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -0.2271 Å / Origin y: 24.6695 Å / Origin z: 45.9916 Å
111213212223313233
T0.2833 Å2-0.0065 Å2-0.006 Å2-0.2527 Å20.0144 Å2--0.251 Å2
L0.4863 °20.1155 °20.0019 °2-0.4009 °20.0623 °2--0.2885 °2
S-0.0107 Å °0.0168 Å °0.0533 Å °-0.1068 Å °-0.0128 Å °0.0247 Å °-0.1141 Å °0.001 Å °-0 Å °
Refinement TLS groupSelection details: all

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