[English] 日本語
Yorodumi
- PDB-8igi: Crystal structure of HP1526 (XthA)- a base excision DNA repair pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8igi
TitleCrystal structure of HP1526 (XthA)- a base excision DNA repair protein in Helicobacter pylori
ComponentsExodeoxyribonuclease (LexA)
KeywordsSTRUCTURAL PROTEIN / H. pylori / DNA damage / DNA repair / BER
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
1,3-BUTANEDIOL / : / Exodeoxyribonuclease (LexA)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsDinh, T.T. / Dao, O. / Lee, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure of the apurinic/apyrimidinic endonuclease XthA (HP1526 protein) from Helicobacter pylori.
Authors: Dinh, T. / Dao, O. / Killivalavan, A. / Ngo, D. / Lee, K.H.
History
DepositionFeb 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exodeoxyribonuclease (LexA)
B: Exodeoxyribonuclease (LexA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3076
Polymers59,0172
Non-polymers2904
Water7,584421
1
A: Exodeoxyribonuclease (LexA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7094
Polymers29,5091
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-4 kcal/mol
Surface area11500 Å2
MethodPISA
2
B: Exodeoxyribonuclease (LexA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5992
Polymers29,5091
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-4 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.096, 71.909, 108.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Exodeoxyribonuclease (LexA)


Mass: 29508.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1526 / Production host: Escherichia coli (E. coli) / References: UniProt: O26054
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG 4K, 104 mM HEPES pH 7.5 with 1,3 butanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→37.05 Å / Num. obs: 49482 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 0.625 / Num. unique obs: 2445

-
Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→37.05 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 2486 5.03 %
Rwork0.1665 --
obs0.168 49383 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 14 421 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084277
X-RAY DIFFRACTIONf_angle_d0.9325760
X-RAY DIFFRACTIONf_dihedral_angle_d15.1462536
X-RAY DIFFRACTIONf_chiral_restr0.064593
X-RAY DIFFRACTIONf_plane_restr0.006737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.87250.28011320.21472310X-RAY DIFFRACTION91
1.8725-1.91070.20281390.19912592X-RAY DIFFRACTION100
1.9107-1.95220.20321350.18732610X-RAY DIFFRACTION100
1.9522-1.99760.24131230.16982628X-RAY DIFFRACTION100
1.9976-2.04760.20211580.16682511X-RAY DIFFRACTION100
2.0476-2.1030.21691290.172573X-RAY DIFFRACTION100
2.103-2.16480.19751560.16412611X-RAY DIFFRACTION100
2.1648-2.23470.19051110.1672610X-RAY DIFFRACTION100
2.2347-2.31460.23231330.16832601X-RAY DIFFRACTION100
2.3146-2.40720.21891480.17752601X-RAY DIFFRACTION100
2.4072-2.51670.20961350.17022612X-RAY DIFFRACTION100
2.5167-2.64940.20681260.17552633X-RAY DIFFRACTION100
2.6494-2.81530.22491470.1812590X-RAY DIFFRACTION100
2.8153-3.03260.21231350.17432645X-RAY DIFFRACTION100
3.0326-3.33760.2021450.16632610X-RAY DIFFRACTION100
3.3376-3.82020.16811370.15342685X-RAY DIFFRACTION100
3.8202-4.81140.15421490.13832671X-RAY DIFFRACTION100
4.8114-37.050.17011480.16732804X-RAY DIFFRACTION100

+
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