[English] 日本語
Yorodumi
- PDB-6nuh: Non-covalent DNA-protein complex between E. coli YedK and ssDNA c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nuh
TitleNon-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog
Components
  • DNA (5'-D(*GP*TP*CP*(PDI)P*GP*GP*A)-3')
  • SOS response-associated peptidase YedK
Keywordsdna binding protein/dna / DNA-protein crosslink / abasic site / thiazolidine / replication stress / DNA BINDING PROTEIN / dna binding protein-dna complex
Function / homology
Function and homology information


protein-DNA covalent cross-linking activity / Lyases / protein-DNA covalent cross-linking repair / SOS response / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / single-stranded DNA binding / DNA damage response / proteolysis
Similarity search - Function
SOS response associated peptidase-like / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / Abasic site processing protein YedK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.594 Å
AuthorsEichman, B.F. / Amidon, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM117299 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01CA092584 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link.
Authors: Thompson, P.S. / Amidon, K.M. / Mohni, K.N. / Cortez, D. / Eichman, B.F.
History
DepositionFeb 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 21, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SOS response-associated peptidase YedK
C: DNA (5'-D(*GP*TP*CP*(PDI)P*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6753
Polymers27,4662
Non-polymers2091
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-2 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.543, 44.129, 55.093
Angle α, β, γ (deg.)90.00, 102.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SOS response-associated peptidase YedK


Mass: 25478.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yedK, yedG, b1931, JW1916 / Production host: Escherichia coli (E. coli)
References: UniProt: P76318, Hydrolases; Acting on peptide bonds (peptidases)
#2: DNA chain DNA (5'-D(*GP*TP*CP*(PDI)P*GP*GP*A)-3') / C3-spacer DNA


Mass: 1987.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 5.4, 23% (w/v) PEG 3350, 0.05 M KH2PO4

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.59→100 Å / Num. obs: 29626 / % possible obs: 98.5 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.042 / Rrim(I) all: 0.086 / Χ2: 1.149 / Net I/σ(I): 21.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2715 / CC1/2: 0.869 / Rpim(I) all: 0.22 / Rrim(I) all: 0.455 / Χ2: 0.541 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NUA

6nua


Resolution: 1.594→39.597 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1773 1481 5 %Random selection
Rwork0.1431 ---
obs0.1447 29612 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.594→39.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 131 14 209 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082007
X-RAY DIFFRACTIONf_angle_d0.9632759
X-RAY DIFFRACTIONf_dihedral_angle_d12.4481162
X-RAY DIFFRACTIONf_chiral_restr0.057282
X-RAY DIFFRACTIONf_plane_restr0.007343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5938-1.64520.20461260.16912391X-RAY DIFFRACTION93
1.6452-1.7040.22291340.16082555X-RAY DIFFRACTION99
1.704-1.77230.19921340.14732529X-RAY DIFFRACTION99
1.7723-1.85290.17511330.14242541X-RAY DIFFRACTION99
1.8529-1.95060.18571340.13542552X-RAY DIFFRACTION99
1.9506-2.07280.16441350.13092559X-RAY DIFFRACTION99
2.0728-2.23280.16021360.13012579X-RAY DIFFRACTION99
2.2328-2.45750.18931340.14342549X-RAY DIFFRACTION99
2.4575-2.8130.17371370.15182618X-RAY DIFFRACTION100
2.813-3.54380.19061380.14742599X-RAY DIFFRACTION100
3.5438-39.60920.15691400.13932659X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -11.0288 Å / Origin y: 8.5181 Å / Origin z: -13.6155 Å
111213212223313233
T0.0767 Å20.0082 Å20.0079 Å2-0.0803 Å2-0.004 Å2--0.0912 Å2
L0.6187 °20.2533 °2-0.2166 °2-0.6957 °2-0.1871 °2--0.9931 °2
S-0.0065 Å °-0.0447 Å °-0.0402 Å °0.0536 Å °-0.0064 Å °-0.0692 Å °0.0415 Å °0.1329 Å °0.0127 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