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- PDB-6fir: Human cytosolic 5'-nucleotidase II soaked with 5mM3-Phenyl-N-(9H-... -

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Basic information

Entry
Database: PDB / ID: 6fir
TitleHuman cytosolic 5'-nucleotidase II soaked with 5mM3-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 / dGMP catabolic process / adenosine metabolic 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 / dGMP catabolic process / adenosine metabolic process / : / amide 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: 2.5 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 ...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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,04612
Polymers64,0891
Non-polymers95711
Water1,38777
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)260,18448
Polymers256,3564
Non-polymers3,82944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area23210 Å2
ΔGint-282 kcal/mol
Surface area73870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.930, 127.680, 130.690
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: 64088.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT CONTAINS RESIDUES 1-536 OUT OF THE 561 AMINO ACIDS OF THE ENZYME. MOREOVER AN N-TERMINAL HISTAG (MGSSHHHHHHSSGLVPRGS) IS PRESENT. A NUMBER OF RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
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: 2.5→50 Å / Num. obs: 25195 / % possible obs: 94.4 % / Redundancy: 4.5 % / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.6 Å / % possible all: 95.2

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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: 2.5→49 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.91
RfactorNum. reflection% reflection
Rfree0.2338 1259 5 %
Rwork0.1792 --
obs0.1819 25186 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 58 77 4001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084017
X-RAY DIFFRACTIONf_angle_d0.9435414
X-RAY DIFFRACTIONf_dihedral_angle_d5.4333298
X-RAY DIFFRACTIONf_chiral_restr0.053573
X-RAY DIFFRACTIONf_plane_restr0.006680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.60030.43171400.32492653X-RAY DIFFRACTION95
2.6003-2.71870.31041370.26512609X-RAY DIFFRACTION94
2.7187-2.8620.33191390.22582636X-RAY DIFFRACTION95
2.862-3.04130.27391400.22372669X-RAY DIFFRACTION95
3.0413-3.2760.26111410.21262666X-RAY DIFFRACTION95
3.276-3.60560.26051380.17672650X-RAY DIFFRACTION95
3.6056-4.12710.19881410.14932677X-RAY DIFFRACTION95
4.1271-5.19880.17671400.13552661X-RAY DIFFRACTION94
5.1988-490.21251430.16732706X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 45.6231 Å / Origin y: -25.0075 Å / Origin z: -19.1953 Å
111213212223313233
T0.3506 Å2-0.013 Å20.0161 Å2-0.3222 Å2-0.013 Å2--0.3273 Å2
L0.4621 °20.1433 °20.0891 °2-0.3552 °2-0.0332 °2--0.3325 °2
S-0.0222 Å °0.0215 Å °-0.0413 Å °-0.1013 Å °-0.0114 Å °-0.0358 Å °0.1197 Å °-0.0072 Å °-0 Å °
Refinement TLS groupSelection details: all

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