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- PDB-5qoz: PanDDA analysis group deposition -- Crystal Structure of DCP2 (NU... -

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Basic information

Entry
Database: PDB / ID: 5qoz
TitlePanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with PB1787571279
ComponentsDCP2 (NUDT20)
KeywordsHYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


RNA exonuclease activity, producing 5'-phosphomonoesters / regulation of telomerase RNA localization to Cajal body / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / mRNA decay by 5' to 3' exoribonuclease / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / 5'-3' RNA exonuclease activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA ...RNA exonuclease activity, producing 5'-phosphomonoesters / regulation of telomerase RNA localization to Cajal body / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / mRNA decay by 5' to 3' exoribonuclease / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / 5'-3' RNA exonuclease activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / RISC complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / KSRP (KHSRP) binds and destabilizes mRNA / mRNA catabolic process / negative regulation of telomere maintenance via telomerase / regulation of mRNA stability / P-body / cytoplasmic ribonucleoprotein granule / cell junction / manganese ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain ...mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-LFG / m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.7 Å
AuthorsNelson, E.R. / Velupillai, S. / Talon, R. / Collins, P.M. / Krojer, T. / Wang, D. / Brandao-Neto, J. / Douangamath, A. / Burgess-Brown, N. / Arrowsmith, C.H. ...Nelson, E.R. / Velupillai, S. / Talon, R. / Collins, P.M. / Krojer, T. / Wang, D. / Brandao-Neto, J. / Douangamath, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Bountra, C. / Huber, K. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Nelson, E.R. / Velupillai, S. / Talon, R. / Collins, P.M. / Krojer, T. / Wang, D. / Brandao-Neto, J. / Douangamath, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Bountra, C. / Huber, K. / von Delft, F.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DCP2 (NUDT20)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6157
Polymers19,0741
Non-polymers5426
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint4 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.125, 60.472, 64.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DCP2 (NUDT20) / Nucleoside diphosphate-linked moiety X motif 20 / Nudix motif 20 / mRNA-decapping enzyme 2 / hDpc / ...Nucleoside diphosphate-linked moiety X motif 20 / Nudix motif 20 / mRNA-decapping enzyme 2 / hDpc / m7GpppN-mRNA hydrolase


Mass: 19073.738 Da / Num. of mol.: 1 / Fragment: UNP residues 95-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCP2, NUDT20 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IU60, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase

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Non-polymers , 5 types, 99 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-LFG / N-cycloheptyl-5-cyclopropyl-1,3,4-oxadiazol-2-amine


Mass: 221.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.48 Å3/Da / Density % sol: 50.35 % / Mosaicity: 0.05 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M acetate, pH 4.5, 5-25% PEG3350

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.7→28.61 Å / Num. obs: 21501 / % possible obs: 99.5 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Rrim(I) all: 0.088 / Net I/σ(I): 13.7 / Num. measured all: 134871 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.745.30.854814315400.7560.4050.9481.997.7
7.59-28.615.50.05715832880.9930.0280.0643298

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5MP0

5mp0


Resolution: 1.7→44.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.042 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1045 4.9 %RANDOM
Rwork0.2167 ---
obs0.2194 20408 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.43 Å2 / Biso mean: 31.623 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0 Å2
2---1.89 Å20 Å2
3---0.79 Å2
Refinement stepCycle: final / Resolution: 1.7→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 36 93 1318
Biso mean--51.44 39.52 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191648
X-RAY DIFFRACTIONr_bond_other_d0.0030.021391
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.9652039
X-RAY DIFFRACTIONr_angle_other_deg1.1452.963226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9415187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.10422.11371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56515241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0451517
X-RAY DIFFRACTIONr_chiral_restr0.1330.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211727
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02348
X-RAY DIFFRACTIONr_mcbond_it3.0082.99762
X-RAY DIFFRACTIONr_mcbond_other3.0022.981756
X-RAY DIFFRACTIONr_mcangle_it4.3514.411901
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 78 -
Rwork0.397 1456 -
all-1534 -
obs--97.46 %

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