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- PDB-6fxh: Human cytosolic 5'-nucleotidase II soaked with 10mM 3-Phenyl-N-(9... -

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Basic information

Entry
Database: PDB / ID: 6fxh
TitleHuman cytosolic 5'-nucleotidase II soaked with 10mM 3-Phenyl-N-(9H-purin-6-yl)benzamide
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 / FOURIER SYNTHESIS / 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
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)65,95212
Polymers65,0551
Non-polymers89711
Water4,017223
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)263,80848
Polymers260,2194
Non-polymers3,58944
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 area24870 Å2
ΔGint-444 kcal/mol
Surface area73810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.900, 128.200, 129.400
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: 65054.684 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 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
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→48.751 Å / Num. obs: 32680 / % possible obs: 96.2 % / Redundancy: 4.2 % / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.4 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2J2C

2j2c


Resolution: 2.3→48.751 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.2349 1632 5.01 %
Rwork0.1771 --
obs0.1799 32600 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 51 223 4185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074052
X-RAY DIFFRACTIONf_angle_d0.8445468
X-RAY DIFFRACTIONf_dihedral_angle_d6.462382
X-RAY DIFFRACTIONf_chiral_restr0.051579
X-RAY DIFFRACTIONf_plane_restr0.005686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.42821330.35422532X-RAY DIFFRACTION95
2.3677-2.44410.38971330.31032520X-RAY DIFFRACTION95
2.4441-2.53150.33491350.26772543X-RAY DIFFRACTION96
2.5315-2.63280.32181360.22432579X-RAY DIFFRACTION97
2.6328-2.75260.2971370.19252613X-RAY DIFFRACTION97
2.7526-2.89770.24851370.18242587X-RAY DIFFRACTION98
2.8977-3.07930.24691380.18012628X-RAY DIFFRACTION98
3.0793-3.3170.25091360.1752583X-RAY DIFFRACTION97
3.317-3.65070.20941370.15262607X-RAY DIFFRACTION96
3.6507-4.17870.17511360.13242583X-RAY DIFFRACTION96
4.1787-5.26370.19381370.14082608X-RAY DIFFRACTION96
5.2637-48.76210.21211370.18412585X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -0.5419 Å / Origin y: 25.1099 Å / Origin z: 45.911 Å
111213212223313233
T0.2322 Å2-0.0194 Å2-0.0042 Å2-0.2078 Å20.0278 Å2--0.2057 Å2
L0.5524 °20.0248 °2-0.1378 °2-0.4369 °20.1403 °2--0.3723 °2
S-0.0028 Å °-0.0113 Å °0.0113 Å °-0.1419 Å °0.0068 Å °0.0192 Å °-0.1211 Å °0.0265 Å °0.0001 Å °
Refinement TLS groupSelection details: (chain A and resseq 2:489)

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