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- PDB-7zeh: Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7G... -

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Basic information

Entry
Database: PDB / ID: 7zeh
TitleHuman cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine
Components7-methylguanosine phosphate-specific 5'-nucleotidase
KeywordsHYDROLASE / Cytosolic 5' nucleotidase / N7 methylguanosine monophosphate dephosphorylation / mRNA cap degradation
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
N7-(3,4-difluorobenzyl) guanine / PHOSPHATE ION / D-ribulose / 7-methylguanosine phosphate-specific 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: 7-methylguanosine phosphate-specific 5'-nucleotidase
C: 7-methylguanosine phosphate-specific 5'-nucleotidase
D: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,07853
Polymers138,7034
Non-polymers4,37549
Water18,9881054
1
A: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69212
Polymers34,6761
Non-polymers1,01611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,63011
Polymers34,6761
Non-polymers95410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,94016
Polymers34,6761
Non-polymers1,26415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 7-methylguanosine phosphate-specific 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81614
Polymers34,6761
Non-polymers1,14013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.590, 80.890, 83.170
Angle α, β, γ (deg.)82.219, 72.462, 68.202
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 6 through 16 or (resid 17...A6 - 18
121(chain 'A' and (resid 6 through 16 or (resid 17...A21 - 161
131(chain 'A' and (resid 6 through 16 or (resid 17...A164 - 166
141(chain 'A' and (resid 6 through 16 or (resid 17...A169 - 207
151(chain 'A' and (resid 6 through 16 or (resid 17...A220 - 229
161(chain 'A' and (resid 6 through 16 or (resid 17...A232 - 253
171(chain 'A' and (resid 6 through 16 or (resid 17...A256 - 289
181(chain 'A' and (resid 6 through 16 or (resid 17...A301
191(chain 'A' and (resid 6 through 16 or (resid 17...A401
1101(chain 'A' and (resid 6 through 16 or (resid 17...A501
1111(chain 'A' and (resid 6 through 16 or (resid 17...A701
1121(chain 'A' and (resid 6 through 16 or (resid 17...A901
1131(chain 'A' and (resid 6 through 16 or (resid 17...A1001
1141(chain 'A' and (resid 6 through 16 or (resid 17...A1401
2151(chain 'B' and (resid 6 through 16 or (resid 17...B6 - 18
2161(chain 'B' and (resid 6 through 16 or (resid 17...B21 - 161
2171(chain 'B' and (resid 6 through 16 or (resid 17...B164 - 166
2181(chain 'B' and (resid 6 through 16 or (resid 17...B169 - 207
2191(chain 'B' and (resid 6 through 16 or (resid 17...B220 - 229
2201(chain 'B' and (resid 6 through 16 or (resid 17...B232 - 253
2211(chain 'B' and (resid 6 through 16 or (resid 17...B256 - 289
2221(chain 'B' and (resid 6 through 16 or (resid 17...B301
2231(chain 'B' and (resid 6 through 16 or (resid 17...B401
2241(chain 'B' and (resid 6 through 16 or (resid 17...B601
2251(chain 'B' and (resid 6 through 16 or (resid 17...B701
2261(chain 'B' and (resid 6 through 16 or (resid 17...B801
2271(chain 'B' and (resid 6 through 16 or (resid 17...B901
2281(chain 'B' and (resid 6 through 16 or (resid 17...B1001
3291(chain 'C' and ((resid 6 and (name N or name...C6 - 18
3301(chain 'C' and ((resid 6 and (name N or name...C21 - 161
3311(chain 'C' and ((resid 6 and (name N or name...C164 - 166
3321(chain 'C' and ((resid 6 and (name N or name...C169 - 207
3331(chain 'C' and ((resid 6 and (name N or name...C220 - 229
3341(chain 'C' and ((resid 6 and (name N or name...C232 - 253
3351(chain 'C' and ((resid 6 and (name N or name...C256 - 289
3361(chain 'C' and ((resid 6 and (name N or name...C301
3371(chain 'C' and ((resid 6 and (name N or name...C401
3381(chain 'C' and ((resid 6 and (name N or name...C601
3391(chain 'C' and ((resid 6 and (name N or name...C701
3401(chain 'C' and ((resid 6 and (name N or name...C801
3411(chain 'C' and ((resid 6 and (name N or name...C1101
3421(chain 'C' and ((resid 6 and (name N or name...C1201
4431(chain 'D' and ((resid 6 and (name N or name...D6 - 18
4441(chain 'D' and ((resid 6 and (name N or name...D21 - 161
4451(chain 'D' and ((resid 6 and (name N or name...D164 - 166
4461(chain 'D' and ((resid 6 and (name N or name...D169 - 207
4471(chain 'D' and ((resid 6 and (name N or name...D220 - 229
4481(chain 'D' and ((resid 6 and (name N or name...D232 - 253
4491(chain 'D' and ((resid 6 and (name N or name...D256 - 289
4501(chain 'D' and ((resid 6 and (name N or name...D301
4511(chain 'D' and ((resid 6 and (name N or name...D401
4521(chain 'D' and ((resid 6 and (name N or name...D901
4531(chain 'D' and ((resid 6 and (name N or name...D1001
4541(chain 'D' and ((resid 6 and (name N or name...D1101
4551(chain 'D' and ((resid 6 and (name N or name...D1201
4561(chain 'D' and ((resid 6 and (name N or name...D2201

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#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.: 4
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
#3: Sugar
ChemComp-RBL / D-ribulose


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 6 types, 1099 molecules

#2: Chemical
ChemComp-IPQ / N7-(3,4-difluorobenzyl) guanine / 2-azanyl-7-[[3,4-bis(fluoranyl)phenyl]methyl]-9H-purin-7-ium-6-ol


Mass: 278.238 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H10F2N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 5.6
Details: 5 % PEG 400, 1.73 M ammonium sulfate, 0.1 M MES pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→75.08 Å / Num. obs: 218378 / % possible obs: 97.54 % / Redundancy: 9.8 % / Biso Wilson estimate: 19.31 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08304 / Rpim(I) all: 0.02803 / Rrim(I) all: 0.08775 / Net I/σ(I): 15.43
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 20240 / CC1/2: 0.732 / CC star: 0.919 / % possible all: 90.31

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Processing

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

2bdu


Resolution: 1.5→75.08 Å / SU ML: 0.1927 / Cross valid method: NONE / σ(F): 0.96 / Phase error: 24.9235 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2199 10917 5 %
Rwork0.1877 409499 -
obs0.1893 218378 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→75.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8683 0 276 1054 10013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139160
X-RAY DIFFRACTIONf_angle_d1.236712362
X-RAY DIFFRACTIONf_chiral_restr0.10111372
X-RAY DIFFRACTIONf_plane_restr0.00841583
X-RAY DIFFRACTIONf_dihedral_angle_d10.3985407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.37146360.346212137X-RAY DIFFRACTION86.25
1.52-1.530.34126460.331512426X-RAY DIFFRACTION87.5
1.53-1.550.33816740.317312736X-RAY DIFFRACTION89.04
1.55-1.570.33276680.294412621X-RAY DIFFRACTION89.92
1.57-1.590.33376860.293412977X-RAY DIFFRACTION91.1
1.59-1.620.27266970.26613127X-RAY DIFFRACTION92.88
1.62-1.640.29796970.264113435X-RAY DIFFRACTION93.91
1.64-1.660.28037080.248313319X-RAY DIFFRACTION94.89
1.66-1.690.26937160.234613685X-RAY DIFFRACTION96.19
1.69-1.720.23887250.217513759X-RAY DIFFRACTION97.3
1.72-1.750.26217260.211413869X-RAY DIFFRACTION98.01
1.75-1.780.24377360.213934X-RAY DIFFRACTION98.43
1.78-1.810.21877400.185814003X-RAY DIFFRACTION98.5
1.81-1.850.23137400.185414035X-RAY DIFFRACTION98.51
1.85-1.890.23667400.180214057X-RAY DIFFRACTION98.67
1.89-1.930.21957290.182413904X-RAY DIFFRACTION98.63
1.93-1.980.25177360.186813955X-RAY DIFFRACTION98.77
1.98-2.040.22677340.164814036X-RAY DIFFRACTION98.74
2.04-2.10.19027380.164213988X-RAY DIFFRACTION98.87
2.1-2.160.20717410.161414025X-RAY DIFFRACTION98.8
2.16-2.240.21087390.160414058X-RAY DIFFRACTION98.75
2.24-2.330.2087330.165613962X-RAY DIFFRACTION98.65
2.33-2.440.21887310.174113958X-RAY DIFFRACTION98.72
2.44-2.560.20847380.172613979X-RAY DIFFRACTION98.76
2.56-2.730.22297350.177813986X-RAY DIFFRACTION98.46
2.73-2.940.20747300.179713933X-RAY DIFFRACTION98.36
2.94-3.230.21767220.182213928X-RAY DIFFRACTION97.72
3.23-3.70.21057310.185213807X-RAY DIFFRACTION97.6
3.7-4.660.17617370.167513935X-RAY DIFFRACTION98.11

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