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

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Basic information

Entry
Database: PDB / ID: 6kij
TitleCrystal structure of yedK with ssDNA containing an abasic site
Components
  • DNA (5'-D(*GP*AP*TP*TP*CP*GP*TP*CP*G)-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
PENTANE-3,4-DIOL-5-PHOSPHATE / DNA / Abasic site processing protein / Abasic site processing protein YedK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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
DepositionJul 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 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 ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

Deposited unit
B: SOS response-associated protein
A: DNA (5'-D(*GP*AP*TP*TP*CP*GP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6464
Polymers28,3542
Non-polymers2922
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-7 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.444, 44.080, 55.148
Angle α, β, γ (deg.)90.00, 102.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SOS response-associated protein / E.coli yedK


Mass: 25606.893 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(*GP*AP*TP*TP*CP*GP*TP*CP*G)-3')


Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-PED / PENTANE-3,4-DIOL-5-PHOSPHATE / OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE


Mass: 200.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2M Ammonium formate 20% w/v PEG3350

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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: 1.579→30 Å / Num. obs: 30514 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 4
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.689 / Num. unique obs: 2980 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KBS

6kbs


Resolution: 1.58→23.17 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.2
RfactorNum. reflection% reflection
Rfree0.183 1546 5.15 %
Rwork0.152 --
obs0.154 29992 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.58→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 59 17 323 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061943
X-RAY DIFFRACTIONf_angle_d0.9012651
X-RAY DIFFRACTIONf_dihedral_angle_d12.8761571
X-RAY DIFFRACTIONf_chiral_restr0.054274
X-RAY DIFFRACTIONf_plane_restr0.005340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.630.24871380.21652205X-RAY DIFFRACTION85
1.63-1.68820.25311520.20182478X-RAY DIFFRACTION96
1.6882-1.75580.21571380.182608X-RAY DIFFRACTION99
1.7558-1.83570.21291450.17122609X-RAY DIFFRACTION99
1.8357-1.93240.19361410.15972588X-RAY DIFFRACTION99
1.9324-2.05340.17741370.14322668X-RAY DIFFRACTION100
2.0534-2.21180.19591470.14632619X-RAY DIFFRACTION100
2.2118-2.43420.18171360.14712625X-RAY DIFFRACTION99
2.4342-2.78590.18741260.15412673X-RAY DIFFRACTION100
2.7859-3.5080.17181460.14232647X-RAY DIFFRACTION99
3.508-23.1740.14761400.13912726X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.7151 Å / Origin y: 5.6189 Å / Origin z: 13.3573 Å
111213212223313233
T0.0905 Å2-0.0034 Å2-0.0021 Å2-0.0965 Å20.004 Å2--0.0957 Å2
L0.5491 °2-0.18 °2-0.0953 °2-0.468 °20.0984 °2--0.7753 °2
S0.0023 Å °0.0303 Å °-0.0294 Å °-0.03 Å °0.0004 Å °0.0517 Å °0.014 Å °-0.1142 Å °0.0065 Å °
Refinement TLS groupSelection details: ALL

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