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- PDB-5qp0: PanDDA analysis group deposition -- Crystal Structure of DCP2 (NU... -

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Basic information

Entry
Database: PDB / ID: 5qp0
TitlePanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z454376544
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-LF4 / m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2 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
DepositionFeb 22, 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)19,6557
Polymers19,0741
Non-polymers5826
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint5 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.540, 60.510, 65.740
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, 85 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-LF4 / N-[(4-fluorophenyl)methyl]-3-(propan-2-yl)-1H-pyrazole-5-carboxamide


Mass: 261.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16FN3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.53 Å3/Da / Density % sol: 51.4 % / Mosaicity: 0 °
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: 2→37.86 Å / Num. obs: 13553 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Net I/σ(I): 15.5 / Num. measured all: 86613 / 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
2-2.056.61.42364179700.6390.5951.5441.699.4
8.94-37.865.30.02100518810.010.02257.297.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5MP0

5mp0


Resolution: 2→44.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.797 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 630 4.7 %RANDOM
Rwork0.2012 ---
obs0.2034 12885 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.41 Å2 / Biso mean: 48.16 Å2 / Biso min: 26.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å20 Å2-0 Å2
2---2.8 Å20 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 2→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 39 79 1313
Biso mean--62.73 49.34 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191885
X-RAY DIFFRACTIONr_bond_other_d0.0030.021547
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9622206
X-RAY DIFFRACTIONr_angle_other_deg1.0432.9733574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.46321.02678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4215289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0561522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02395
X-RAY DIFFRACTIONr_mcbond_it3.9694.647855
X-RAY DIFFRACTIONr_mcbond_other3.8874.61839
X-RAY DIFFRACTIONr_mcangle_it6.2816.825970
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 52 -
Rwork0.331 914 -
all-966 -
obs--99.08 %

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