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- PDB-6kbx: Crystal structure of yedK in complex with ssDNA containing abasic site -

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Basic information

Entry
Database: PDB / ID: 6kbx
TitleCrystal structure of yedK in complex with ssDNA containing abasic site
Components
  • DNA 5'-D (*CP*GP*GP*TP* (PED)P*GP*AP*TP*TP*C)-3'
  • SOS response-associated protein
KeywordsDNA BINDING PROTEIN / DNA repair / abasic site / 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 / Abasic site processing protein YedK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.221 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 26, 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 13, 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 (*CP*GP*GP*TP* (PED)P*GP*AP*TP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)28,5362
Polymers28,5362
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-5 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.092, 44.084, 54.731
Angle α, β, γ (deg.)90.000, 101.690, 90.000
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 (*CP*GP*GP*TP* (PED)P*GP*AP*TP*TP*C)-3'


Mass: 2928.920 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.: 302 / 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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M sodium formate, 20% 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: 1.22→50 Å / Num. obs: 64468 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.19 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Χ2: 1.035 / Net I/σ(I): 5.1 / Num. measured all: 416830
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.22-1.264.60.61960720.6760.2990.6911.03693.6
1.26-1.3160.56564400.8010.2460.6181.0599.1
1.31-1.376.40.45463850.8820.1930.4941.0998.4
1.37-1.456.80.33864640.9240.1390.3661.06999.9
1.45-1.546.70.25264940.9570.1040.2731.08499.6
1.54-1.666.60.18864120.9740.0780.2041.0798.5
1.66-1.826.90.13965310.9840.0570.151.04899.9
1.82-2.096.70.09864490.9920.040.1060.97999
2.09-2.6370.08365580.9930.0340.090.871100
2.63-506.80.06566630.9950.0270.0711.06599.5

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Processing

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

6kbs


Resolution: 1.221→46.115 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.98
RfactorNum. reflection% reflection
Rfree0.1647 2984 5.01 %
Rwork0.1552 --
obs0.1557 59603 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.34 Å2 / Biso mean: 20.5304 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: final / Resolution: 1.221→46.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 79 0 302 2192
Biso mean---31.9 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051955
X-RAY DIFFRACTIONf_angle_d0.922674
X-RAY DIFFRACTIONf_chiral_restr0.075276
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d18.091723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2213-1.24140.3662530.323883789029
1.2414-1.26280.2871730.28691478155151
1.2628-1.28570.2673950.26342053214869
1.2857-1.31050.22731180.2322512263085
1.3105-1.33720.2691580.22272779293794
1.3372-1.36630.22931540.20832793294796
1.3663-1.39810.21151350.18729503085100
1.3981-1.4330.18231640.179929653129100
1.433-1.47180.17451530.175329233076100
1.4718-1.51510.17131670.165529053072100
1.5151-1.5640.16471470.15892924307199
1.564-1.61990.18241520.15662875302798
1.6199-1.68480.16841490.159229443093100
1.6848-1.76140.15331610.153129503111100
1.7614-1.85430.1651710.14929203091100
1.8543-1.97050.16331600.14872911307199
1.9705-2.12260.15131540.14322933308799
2.1226-2.33620.17641580.144429573115100
2.3362-2.67430.16821620.156529743136100
2.6743-3.36910.15621520.14642989314199
3.3691-46.14740.13861480.144230473195100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59690.3075-0.08391.52860.50350.7612-0.03070.00460.0062-0.0620.0538-0.0468-0.04230.0151-0.02610.11680.002-0.00550.12740.00070.117319.138410.331916.9102
23.13392.1621-0.11915.7162-0.1321.62950.0262-0.0936-0.09790.18160.01370.17860.0747-0.1708-0.03590.08020.01670.01040.12780.01160.06076.2125.041124.0653
30.780.46962.13532.87960.86156.3125-0.02370.03330.05870.0239-0.0740.3073-0.0604-0.52820.13790.10210.0040.0030.2188-0.0050.1837-4.69295.226615.6655
46.037-0.3273-4.05632.33311.40434.85660.04120.01790.0457-0.0015-0.07260.2151-0.0619-0.2141-0.00210.11990.0094-0.0190.11240.0190.10154.781311.658317.8106
50.7914-0.2867-0.57090.61210.07792.41260.00980.0691-0.0618-0.0393-0.0150.05020.1301-0.08110.03020.0982-0.0153-0.01840.1074-0.00340.122411.59951.171711.1406
63.36770.18310.21624.06024.72617.98980.07530.3188-0.0905-0.3557-0.07540.0379-0.1978-0.40290.03880.1227-0.0058-0.00960.13390.00710.12364.72152.344.8262
71.04480.11770.18751.81310.62852.38560.03330.04970.0718-0.0359-0.0656-0.036-0.1592-0.20050.0790.11450.02380.00140.1850.01450.13276.055113.398810.483
85.691-5.963-3.65566.47343.78454.09020.20570.3166-0.0154-0.2973-0.240.1463-0.2802-0.4950.00210.13960.0051-0.03230.19420.0060.1295.921910.70473.3236
97.5813-4.0944-0.93825.8111-2.72323.0567-0.1047-0.2005-0.17840.07620.0434-0.04960.0835-0.03210.05870.1233-0.014-0.00210.06910.01280.114821.3772-9.406911.4071
100.01490.11280.28774.52134.19544.5964-0.01880.0281-0.01970.0859-0.02060.10860.16150.0339-0.00610.17950.00040.00280.15340.00040.163223.2907-8.82681.159
117.1787-1.1918-5.28544.33571.28233.9979-0.3887-0.1986-0.2060.5330.32110.94540.7621-0.84220.07810.2303-0.04280.07520.36010.02810.3139-7.3221-1.802319.9095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 50 )B2 - 50
2X-RAY DIFFRACTION2chain 'B' and (resid 51 through 74 )B51 - 74
3X-RAY DIFFRACTION3chain 'B' and (resid 75 through 87 )B75 - 87
4X-RAY DIFFRACTION4chain 'B' and (resid 88 through 101 )B88 - 101
5X-RAY DIFFRACTION5chain 'B' and (resid 102 through 144 )B102 - 144
6X-RAY DIFFRACTION6chain 'B' and (resid 145 through 158 )B145 - 158
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 181 )B159 - 181
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 203 )B182 - 203
9X-RAY DIFFRACTION9chain 'B' and (resid 204 through 215 )B204 - 215
10X-RAY DIFFRACTION10chain 'B' and (resid 216 through 227 )B216 - 227
11X-RAY DIFFRACTION11chain 'A' and (resid -2 through 1 )A-2 - 1

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