[English] 日本語
Yorodumi
- PDB-5vy2: Crystal structure of the F36A mutant of HsNUDT16 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vy2
TitleCrystal structure of the F36A mutant of HsNUDT16
ComponentsU8 snoRNA-decapping enzyme
KeywordsHYDROLASE / nudix / nudix hydrolase / decapping enzyme / demodification of parylation / demodification of marylation / ADPribose / di-ADPribose
Function / homology
Function and homology information


inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing / NAD-cap decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Phosphate bond hydrolysis by NUDT proteins / metalloexopeptidase activity / cobalt ion binding / chloride ion binding / snoRNA binding / mRNA catabolic process / manganese ion binding / nucleotide binding / mRNA binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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
U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsThirawatananond, P. / Gabelli, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
AHN United States
DOD United States
CitationJournal: Sci Rep / Year: 2019
Title: Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
Authors: Thirawatananond, P. / McPherson, R.L. / Malhi, J. / Nathan, S. / Lambrecht, M.J. / Brichacek, M. / Hergenrother, P.J. / Leung, A.K.L. / Gabelli, S.B.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U8 snoRNA-decapping enzyme
B: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5323
Polymers42,5092
Non-polymers231
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer AB
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-24 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.202, 49.589, 64.284
Angle α, β, γ (deg.)90.000, 114.590, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein U8 snoRNA-decapping enzyme / IDP phosphatase / IDPase / Inosine diphosphate phosphatase / Nucleoside diphosphate-linked moiety X ...IDP phosphatase / IDPase / Inosine diphosphate phosphatase / Nucleoside diphosphate-linked moiety X motif 16 / Nudix motif 16 / U8 snoRNA-binding protein H29K / m7GpppN-mRNA hydrolase


Mass: 21254.330 Da / Num. of mol.: 2 / Mutation: A22V, F36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIPL
References: UniProt: Q96DE0, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, inosine diphosphate phosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.95 Å3/Da / Density % sol: 36.79 % / Mosaicity: 1.298 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: PEG 8000, CHES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13719 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.055 / Rrim(I) all: 0.09 / Χ2: 4.229 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.341.70.1350.9560.1230.1832.77274.3
2.34-2.3820.1430.9460.1160.1852.80981.3
2.38-2.432.20.1480.960.1160.1893.28187.3
2.43-2.482.60.1470.9640.1080.1843.13492.6
2.48-2.532.70.1290.9730.0950.1613.56992.8
2.53-2.592.70.1260.9680.0940.1583.93793.3
2.59-2.662.70.1220.9830.090.1533.58593.2
2.66-2.732.70.120.9780.0880.1493.894.1
2.73-2.812.70.1160.9780.0860.1454.05195.1
2.81-2.92.70.1090.980.0820.1374.22694
2.9-32.70.0990.9820.0760.1254.26195.6
3-3.122.70.0860.9850.0670.1094.23496.1
3.12-3.262.70.0780.9870.0590.0984.47195.6
3.26-3.442.70.0660.9880.0510.0844.87996.5
3.44-3.652.50.060.990.0480.0774.64195.1
3.65-3.932.60.0610.9890.0490.0795.10991.9
3.93-4.332.40.0540.9910.0430.0695.0191.3
4.33-4.952.40.0550.9920.0450.0715.2493.1
4.95-6.242.50.0580.9890.0460.0745.20294.1
6.24-502.30.0510.9920.0430.0674.97792.2

-
Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
REFMACphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdbid XX

Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.275 / SU ML: 0.178 / SU R Cruickshank DPI: 0.691 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.691 / ESU R Free: 0.288
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 633 4.6 %RANDOM
Rwork0.1889 ---
obs0.1919 13077 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.64 Å2 / Biso mean: 29.92 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å2-0.39 Å2
2---0.84 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 1 176 2942
Biso mean--44.28 29.84 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192840
X-RAY DIFFRACTIONr_bond_other_d0.0020.022736
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9873837
X-RAY DIFFRACTIONr_angle_other_deg0.98636268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81521.533137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91615477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9931540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
LS refinement shellResolution: 2.29→2.349 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 44 -
Rwork0.22 739 -
all-783 -
obs--72.7 %

+
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