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- PDB-7zee: Human cytosolic 5' nucleotidase IIIB -

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Basic information

Entry
Database: PDB / ID: 7zee
TitleHuman cytosolic 5' nucleotidase IIIB
Components7-methylguanosine phosphate-specific 5'-nucleotidase
KeywordsHYDROLASE / cytosolic 5' nucleotidase / N7 methylguanosine monophosphate dephosphorylation / mRNA cap degradation / nucleotide level regulation
Function / homology
Function and homology information


7-methylguanosine nucleotidase / mRNA decay by 3' to 5' exoribonuclease / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nucleotide binding / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
7-methylguanosine phosphate-specific 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKubacka, D. / Kozarski, M. / Baranowski, M.R. / Wojcik, R. / Jemielity, J. / Kowalska, J. / Basquin, J.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO- 2017/24/C/NZ1/00169 Poland
CitationJournal: Pharmaceuticals / Year: 2022
Title: Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.
Authors: Kubacka, D. / Kozarski, M. / Baranowski, M.R. / Wojcik, R. / Panecka-Hofman, J. / Strzelecka, D. / Basquin, J. / Jemielity, J. / Kowalska, J.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jun 8, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70216
Polymers34,6761
Non-polymers1,02615
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint31 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.715, 79.288, 87.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 7-methylguanosine phosphate-specific 5'-nucleotidase / 7-methylguanosine nucleotidase / Cytosolic 5'-nucleotidase 3B / Cytosolic 5'-nucleotidase III-like ...7-methylguanosine nucleotidase / Cytosolic 5'-nucleotidase 3B / Cytosolic 5'-nucleotidase III-like protein / cN-III-like protein / N(7)-methylguanylate 5'-phosphatase


Mass: 34675.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C3B, NT5C3L / Production host: Escherichia coli (E. coli)
References: UniProt: Q969T7, 7-methylguanosine nucleotidase, 5'-nucleotidase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.2 / Details: 0.1 M MES pH 6.2, 27% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.357→38.24 Å / Num. obs: 60466 / % possible obs: 95.2 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05247 / Rpim(I) all: 0.01559 / Rrim(I) all: 0.05482 / Net I/σ(I): 25.78
Reflection shellResolution: 1.357→1.405 Å / Mean I/σ(I) obs: 1.68 / Num. unique obs: 4228 / CC1/2: 0.824 / CC star: 0.951

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bdu

2bdu


Resolution: 1.36→38.24 Å / SU ML: 0.1388 / Cross valid method: NONE / σ(F): 1.26 / Phase error: 20.5307 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 5732 5 %
Rwork0.1586 108815 -
obs0.1605 60466 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.56 Å2
Refinement stepCycle: LAST / Resolution: 1.36→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 65 295 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172382
X-RAY DIFFRACTIONf_angle_d1.21963199
X-RAY DIFFRACTIONf_chiral_restr0.0957352
X-RAY DIFFRACTIONf_plane_restr0.0075411
X-RAY DIFFRACTIONf_dihedral_angle_d10.82971425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.370.4524770.44021467X-RAY DIFFRACTION38.62
1.37-1.390.36031420.3052709X-RAY DIFFRACTION68.86
1.39-1.40.27651580.25432898X-RAY DIFFRACTION76.51
1.4-1.420.2851580.23643114X-RAY DIFFRACTION80.95
1.42-1.440.22511700.21023306X-RAY DIFFRACTION85.28
1.44-1.460.25871820.19753438X-RAY DIFFRACTION91.05
1.46-1.480.24461880.18413618X-RAY DIFFRACTION94.07
1.48-1.50.2021990.17223770X-RAY DIFFRACTION98.54
1.5-1.530.21862010.16873881X-RAY DIFFRACTION99.95
1.53-1.550.21962030.15423829X-RAY DIFFRACTION99.98
1.55-1.580.17682030.14993817X-RAY DIFFRACTION99.95
1.58-1.610.24192030.16123912X-RAY DIFFRACTION99.95
1.61-1.640.20212050.14513777X-RAY DIFFRACTION99.92
1.64-1.670.19871990.15173853X-RAY DIFFRACTION99.95
1.67-1.710.2221980.14373811X-RAY DIFFRACTION99.93
1.71-1.750.1982080.13853870X-RAY DIFFRACTION99.98
1.75-1.790.20592000.13183845X-RAY DIFFRACTION100
1.79-1.840.18672040.13183805X-RAY DIFFRACTION100
1.84-1.890.16492060.13373894X-RAY DIFFRACTION100
1.89-1.960.18462010.13973813X-RAY DIFFRACTION100
1.96-2.030.15752040.14583809X-RAY DIFFRACTION99.98
2.03-2.110.16982050.14273846X-RAY DIFFRACTION100
2.11-2.20.19162030.14533858X-RAY DIFFRACTION99.98
2.2-2.320.18841960.14493858X-RAY DIFFRACTION99.98
2.32-2.460.22072010.15723834X-RAY DIFFRACTION99.95
2.46-2.650.20092030.15943830X-RAY DIFFRACTION100
2.65-2.920.19611990.16333829X-RAY DIFFRACTION100
2.92-3.340.17642030.1643834X-RAY DIFFRACTION100
3.34-4.210.18182090.15043856X-RAY DIFFRACTION99.98

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