[English] 日本語
Yorodumi
- PDB-5qok: PanDDA analysis group deposition -- Crystal Structure of DCP2 (NU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qok
TitlePanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000294a
ComponentsDCP2 (NUDT20)
KeywordsHYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


exoribonuclease 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'-3' exoribonuclease activity / exonucleolytic catabolism of deadenylated mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / m7G(5')pppN diphosphatase activity / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA ...exoribonuclease 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'-3' exoribonuclease activity / exonucleolytic catabolism of deadenylated mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / m7G(5')pppN diphosphatase activity / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / histone mRNA catabolic process / deadenylation-dependent decapping of nuclear-transcribed mRNA / telomerase RNA binding / RISC complex / negative regulation of telomere maintenance via telomerase / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / mRNA catabolic process / regulation of mRNA stability / P-body / cytoplasmic ribonucleoprotein granule / cell junction / manganese ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Dcp2, box A domain / Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping protein 2, Box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain ...Dcp2, box A domain / Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping protein 2, Box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / 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-AWS / DI(HYDROXYETHYL)ETHER / m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.28 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DCP2 (NUDT20)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6717
Polymers19,0741
Non-polymers5986
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint7 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.160, 61.090, 65.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
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

-
Non-polymers , 6 types, 73 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-AWS / 8-[(dimethylamino)methyl]-4-methyl-7-oxidanyl-chromen-2-one


Mass: 233.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 % / 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

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.28→37.82 Å / Num. obs: 9314 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.075 / Rrim(I) all: 0.192 / Net I/σ(I): 8.8 / Num. measured all: 59810 / 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
2.28-2.346.30.81241326600.7860.350.8862.499.7
10.2-37.825.40.0476971300.9980.0220.05226.998.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5MP0
Resolution: 2.28→44.79 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.842 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2706 433 4.7 %RANDOM
Rwork0.2026 ---
obs0.2056 8846 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.73 Å2 / Biso mean: 39.123 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å2-0 Å2
2---3.71 Å20 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 2.28→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 40 67 1297
Biso mean--58.17 41.4 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191744
X-RAY DIFFRACTIONr_bond_other_d0.0020.021397
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9572085
X-RAY DIFFRACTIONr_angle_other_deg0.9922.9723232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3422.43274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8615247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3141517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211803
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
X-RAY DIFFRACTIONr_mcbond_it2.5253.878815
X-RAY DIFFRACTIONr_mcbond_other2.5673.873787
X-RAY DIFFRACTIONr_mcangle_it4.2935.735925
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 33 -
Rwork0.306 624 -
all-657 -
obs--99.7 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more