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- PDB-6kcq: Crystal structure of yedK with ssDNA containing an abasic site -

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Basic information

Entry
Database: PDB / ID: 6kcq
TitleCrystal structure of yedK with ssDNA containing an abasic site
Components
  • DNA (5'-D(P*AP*AP*AP*(PED)P*AP*A)-3')
  • SOS response-associated protein
KeywordsDNA BINDING PROTEIN / DNA repair / abasic site
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 / DNA (> 10) / Abasic site processing protein / Abasic site processing protein YedK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsWang, N. / Bao, H. / Huang, H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFC1004500 China
National Natural Science Foundation of Chinathe Thousand Young Talents Program China
National Natural Science Foundation of China31800619 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.
Authors: Wang, N. / Bao, H. / Chen, L. / Liu, Y. / Li, Y. / Wu, B. / Huang, H.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Nov 22, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: SOS response-associated protein
A: DNA (5'-D(P*AP*AP*AP*(PED)P*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)29,0072
Polymers29,0072
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.671, 70.671, 44.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein SOS response-associated protein / yedk


Mass: 25738.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yedK, C4J69_22885, ECTO6_01993, EFV06_12905, EFV16_12155, SAMEA3472108_01185, SAMEA3752559_04370
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2S5ZH06, UniProt: P76318*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: DNA chain DNA (5'-D(P*AP*AP*AP*(PED)P*AP*A)-3')


Mass: 3269.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.67 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.05M calcium chloride dihydrate 0.1M Bis-Tris pH6.5 30% MPEG550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 24080 / % possible obs: 99.1 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Net I/σ(I): 23
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.409 / Num. unique obs: 2271 / CC1/2: 0.444 / Rpim(I) all: 0.22 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6kbs

6kbs


Resolution: 1.701→37.61 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 17.92
RfactorNum. reflection% reflection
Rfree0.204 1070 4.73 %
Rwork0.1602 --
obs0.1624 22607 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 116 0 218 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071941
X-RAY DIFFRACTIONf_angle_d0.8852652
X-RAY DIFFRACTIONf_dihedral_angle_d14.8081122
X-RAY DIFFRACTIONf_chiral_restr0.054273
X-RAY DIFFRACTIONf_plane_restr0.005333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7008-1.77830.2513710.21811686X-RAY DIFFRACTION58
1.7783-1.8720.24551260.20672495X-RAY DIFFRACTION89
1.872-1.98930.22691490.18452853X-RAY DIFFRACTION99
1.9893-2.14290.23621200.1662912X-RAY DIFFRACTION100
2.1429-2.35850.19541320.15092870X-RAY DIFFRACTION100
2.3585-2.69970.20091690.15692865X-RAY DIFFRACTION100
2.6997-3.4010.20491520.14712889X-RAY DIFFRACTION100
3.401-37.6190.17461510.14422967X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.1299 Å / Origin y: 60.7069 Å / Origin z: -5.748 Å
111213212223313233
T0.0205 Å20.0038 Å2-0.0087 Å2-0.053 Å20.0184 Å2--0.0676 Å2
L1.1341 °20.5885 °2-0.0975 °2-2.3436 °2-0.4004 °2--1.5143 °2
S-0.0189 Å °-0.0227 Å °0.0777 Å °0.0006 Å °0.0763 Å °0.354 Å °-0.0012 Å °-0.1993 Å °-0.0119 Å °
Refinement TLS groupSelection details: all

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