[English] 日本語
Yorodumi
- PDB-7jw2: Crystal structure of Aedes aegypti Nibbler EXO domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jw2
TitleCrystal structure of Aedes aegypti Nibbler EXO domain
ComponentsExonuclease mut-7 homolog
KeywordsRNA BINDING PROTEIN / Nibbler / exoribonuclease / microRNA trimming / piRNA trimming
Function / homology
Function and homology information


3'-5' exonuclease activity / Hydrolases; Acting on ester bonds / nucleic acid binding / metal ion binding
Similarity search - Function
Exonuclease Mut-7, DEDDy 3'-5' exonuclease domain / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Exonuclease mut-7 homolog
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsXie, W. / Sowemimo, I. / Hayashi, R. / Wang, J. / Brennecke, J. / Ameres, S.L. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure-function analysis of microRNA 3'-end trimming by Nibbler.
Authors: Xie, W. / Sowemimo, I. / Hayashi, R. / Wang, J. / Burkard, T.R. / Brennecke, J. / Ameres, S.L. / Patel, D.J.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exonuclease mut-7 homolog
B: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)52,2592
Polymers52,2592
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.508, 71.584, 83.031
Angle α, β, γ (deg.)90.000, 97.320, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Exonuclease mut-7 homolog / Exonuclease 3'-5' domain-containing protein 3 homolog


Mass: 26129.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL005527 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q179T2, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium formate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→37.28 Å / Num. obs: 72680 / % possible obs: 98.85 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.03341 / Rpim(I) all: 0.01727 / Rrim(I) all: 0.03775 / Net I/σ(I): 26.22
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1528 / Mean I/σ(I) obs: 5.74 / Num. unique obs: 6711 / CC1/2: 0.983 / CC star: 0.996 / Rpim(I) all: 0.09235 / Rrim(I) all: 0.1796 / % possible all: 91.92

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Drosophila Nbr EXO domain

Resolution: 1.5→37.28 Å / SU ML: 0.1501 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.9256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 3628 5 %
Rwork0.1916 68941 -
obs0.1924 72569 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 0 425 3977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563632
X-RAY DIFFRACTIONf_angle_d0.79794925
X-RAY DIFFRACTIONf_chiral_restr0.0504549
X-RAY DIFFRACTIONf_plane_restr0.0046632
X-RAY DIFFRACTIONf_dihedral_angle_d5.6868467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.26811400.22352336X-RAY DIFFRACTION86.66
1.52-1.540.26221350.21622427X-RAY DIFFRACTION93.23
1.54-1.560.23311300.21172648X-RAY DIFFRACTION98.9
1.56-1.590.26061390.21312690X-RAY DIFFRACTION99.79
1.59-1.610.22781410.20942658X-RAY DIFFRACTION99.86
1.61-1.640.26951510.21332677X-RAY DIFFRACTION99.79
1.64-1.670.22711480.20642652X-RAY DIFFRACTION99.89
1.67-1.70.27541200.21462647X-RAY DIFFRACTION99.75
1.7-1.730.26591560.21042680X-RAY DIFFRACTION99.86
1.73-1.760.22881350.20772684X-RAY DIFFRACTION99.89
1.76-1.80.23081540.21372652X-RAY DIFFRACTION99.72
1.8-1.840.23271200.20732668X-RAY DIFFRACTION99.61
1.84-1.890.20781310.20552693X-RAY DIFFRACTION99.65
1.89-1.940.20891310.20872662X-RAY DIFFRACTION99.79
1.94-20.23891390.20762686X-RAY DIFFRACTION99.86
2-2.060.24181440.20892669X-RAY DIFFRACTION99.93
2.06-2.140.2181270.20442676X-RAY DIFFRACTION99.82
2.14-2.220.22431440.19862680X-RAY DIFFRACTION99.75
2.22-2.320.21821180.1932705X-RAY DIFFRACTION99.54
2.32-2.450.23331260.20812671X-RAY DIFFRACTION99.5
2.45-2.60.23031520.2042660X-RAY DIFFRACTION99.5
2.6-2.80.24271660.19262646X-RAY DIFFRACTION99.01
2.8-3.080.19621410.19942677X-RAY DIFFRACTION99.47
3.08-3.530.19361470.18162687X-RAY DIFFRACTION99.61
3.53-4.440.16491350.15952709X-RAY DIFFRACTION99.51
4.44-37.280.16291580.17192701X-RAY DIFFRACTION98.52

+
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