[English] 日本語
Yorodumi
- PDB-6a4b: Structure of TREX2 in complex with a duplex DNA with 2 nucleotide... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a4b
TitleStructure of TREX2 in complex with a duplex DNA with 2 nucleotide 3'-overhang
Components
  • DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
  • Three prime repair exonuclease 2
KeywordsDNA BINDING PROTEIN / Exonuclease / DEDDh exonuclease
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / DNA catabolic process / DNA metabolic process / nucleic acid binding / DNA repair / magnesium ion binding / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Three prime repair exonuclease 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHsiao, Y.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
MOST 106-2311-B-009-002 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural insights into the duplex DNA processing of TREX2
Authors: Cheng, H.L. / Lin, C.T. / Huang, K.W. / Wang, S. / Lin, Y.T. / Toh, S.I. / Hsiao, Y.Y.
History
DepositionJun 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Three prime repair exonuclease 2
B: Three prime repair exonuclease 2
C: Three prime repair exonuclease 2
D: Three prime repair exonuclease 2
E: Three prime repair exonuclease 2
F: Three prime repair exonuclease 2
G: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
H: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
I: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
J: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
K: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
L: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,05623
Polymers201,78812
Non-polymers26711
Water57632
1
A: Three prime repair exonuclease 2
B: Three prime repair exonuclease 2
G: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
H: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3608
Polymers67,2634
Non-polymers974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-45 kcal/mol
Surface area22720 Å2
MethodPISA
2
C: Three prime repair exonuclease 2
D: Three prime repair exonuclease 2
I: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
J: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3367
Polymers67,2634
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-33 kcal/mol
Surface area23670 Å2
MethodPISA
3
E: Three prime repair exonuclease 2
F: Three prime repair exonuclease 2
K: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
L: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3608
Polymers67,2634
Non-polymers974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-41 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.715, 87.317, 432.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Three prime repair exonuclease 2 / 3'-5' exonuclease TREX2


Mass: 28156.832 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R1A9, exodeoxyribonuclease III
#2: DNA chain
DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')


Mass: 5474.526 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.5, 22%(w/v) Polyethylene glycol 1,000, 0.1M Barium chloride dihydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 51078 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.04 / Rsym value: 0.078 / Net I/σ(I): 23.45
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 4998 / Rpim(I) all: 0.31 / Rsym value: 0.581 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y97

1y97


Resolution: 2.7→29.233 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 3961 7.8 %
Rwork0.2243 --
obs0.2274 50754 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10082 1857 11 32 11982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312397
X-RAY DIFFRACTIONf_angle_d0.68717200
X-RAY DIFFRACTIONf_dihedral_angle_d17.4534658
X-RAY DIFFRACTIONf_chiral_restr0.0251932
X-RAY DIFFRACTIONf_plane_restr0.0031928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73290.38991370.34551600X-RAY DIFFRACTION97
2.7329-2.76750.34721380.35531610X-RAY DIFFRACTION97
2.7675-2.80390.37121530.34111630X-RAY DIFFRACTION98
2.8039-2.84220.39021580.32811697X-RAY DIFFRACTION98
2.8422-2.88280.36111350.3171655X-RAY DIFFRACTION98
2.8828-2.92580.36261530.30731624X-RAY DIFFRACTION97
2.9258-2.97150.33741340.31191644X-RAY DIFFRACTION98
2.9715-3.02010.32511360.30011716X-RAY DIFFRACTION99
3.0201-3.07220.29441310.2981643X-RAY DIFFRACTION98
3.0722-3.1280.34211500.27731684X-RAY DIFFRACTION98
3.128-3.18810.30361520.27471646X-RAY DIFFRACTION99
3.1881-3.25310.31511400.26771718X-RAY DIFFRACTION99
3.2531-3.32370.30351280.26631644X-RAY DIFFRACTION98
3.3237-3.40090.31711400.26811665X-RAY DIFFRACTION98
3.4009-3.48580.28431400.25131720X-RAY DIFFRACTION98
3.4858-3.57990.28491360.23151629X-RAY DIFFRACTION98
3.5799-3.6850.27391380.23681688X-RAY DIFFRACTION98
3.685-3.80370.26931440.24021686X-RAY DIFFRACTION98
3.8037-3.93940.27181370.22211661X-RAY DIFFRACTION98
3.9394-4.09670.27591080.21051714X-RAY DIFFRACTION97
4.0967-4.28260.2151370.2071660X-RAY DIFFRACTION98
4.2826-4.50760.24941350.19181707X-RAY DIFFRACTION97
4.5076-4.78890.22681530.19081681X-RAY DIFFRACTION97
4.7889-5.15680.25871460.18831692X-RAY DIFFRACTION97
5.1568-5.67230.26661430.19681734X-RAY DIFFRACTION98
5.6723-6.48530.26071620.21031717X-RAY DIFFRACTION98
6.4853-8.14150.19731560.19271771X-RAY DIFFRACTION97
8.1415-29.23460.21621410.18651557X-RAY DIFFRACTION82
Refinement TLS params.Method: refined / Origin x: -13.6746 Å / Origin y: -23.6668 Å / Origin z: -54.2933 Å
111213212223313233
T0.4339 Å2-0.0245 Å2-0.0192 Å2-0.5228 Å2-0.0779 Å2--0.5538 Å2
L0.395 °2-0.3087 °2-0.2222 °2-1.1214 °20.829 °2--1.3646 °2
S-0.0277 Å °0.1822 Å °-0.0045 Å °0.1369 Å °-0.0188 Å °-0.0682 Å °-0.1318 Å °-0.012 Å °0.0479 Å °
Refinement TLS groupSelection details: all

+
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