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- PDB-6kbs: Crystal structure of yedK in complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 6kbs
TitleCrystal structure of yedK in complex with ssDNA
Components
  • DNA (5'-D(*CP*GP*GP*TP*CP*GP*AP*TP*TP*C)-3')
  • SOS response-associated protein
KeywordsDNA BINDING PROTEIN / DNA repair. abasic site.
Function / homology
Function and homology information


: / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / single-stranded DNA binding / DNA damage response
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6432
Polymers28,6432
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-5 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.890, 50.322, 54.531
Angle α, β, γ (deg.)90.000, 99.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-101-

HOH

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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, Hydrolases; Acting on peptide bonds (peptidases)
#2: DNA chain DNA (5'-D(*CP*GP*GP*TP*CP*GP*AP*TP*TP*C)-3')


Mass: 3035.990 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.: 237 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.1 M Citric pH 4.0, 3% PEG6000

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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: 1.6→40 Å / Num. obs: 32253 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.98 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Χ2: 0.479 / Net I/σ(I): 4.8 / Num. measured all: 214311
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.665.90.60232020.8620.2620.6590.42499.6
1.66-1.726.60.47532230.9290.1970.5150.431100
1.72-1.86.50.33732250.960.1420.3670.46199.4
1.8-1.96.70.23631750.9770.0970.2560.49199.2
1.9-2.026.90.17132520.9870.070.1850.47999.9
2.02-2.176.60.11732060.9930.0490.1270.50299.3
2.17-2.396.90.08632170.9950.0350.0930.51299.4
2.39-2.746.80.06632210.9970.0270.0720.51599.6
2.74-3.456.90.04332400.9990.0170.0460.50499.1
3.45-406.70.03332920.9990.0140.0350.45598.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KBU

6kbu


Resolution: 1.601→37.757 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.22
RfactorNum. reflection% reflection
Rfree0.2008 1608 4.99 %
Rwork0.1728 --
obs0.1742 32237 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.6 Å2 / Biso mean: 28.2673 Å2 / Biso min: 10.06 Å2
Refinement stepCycle: final / Resolution: 1.601→37.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 185 0 237 2232
Biso mean---35.43 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072103
X-RAY DIFFRACTIONf_angle_d0.8452901
X-RAY DIFFRACTIONf_chiral_restr0.053299
X-RAY DIFFRACTIONf_plane_restr0.005355
X-RAY DIFFRACTIONf_dihedral_angle_d13.2121641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6013-1.6530.26831460.27172706285296
1.653-1.71210.29271540.236927692923100
1.7121-1.78060.2341520.214427562908100
1.7806-1.86160.21781440.19062772291699
1.8616-1.95980.21951610.190327862947100
1.9598-2.08260.25381310.186328092940100
2.0826-2.24330.20841510.17682761291299
2.2433-2.46910.21731300.176928092939100
2.4691-2.82620.19831360.18312784292099
2.8262-3.56030.17861400.163628452985100
3.5603-37.76720.17551630.14382832299599
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)
13.4609-0.26932.66051.2610.0924.2077-0.06060.13640.2366-0.1214-0.0650.1339-0.30850.10070.15250.1694-0.0228-0.01190.14170.02410.1507-18.804511.41377.8634
22.1803-0.59571.24771.9912-0.26843.5421-0.029-0.115-0.03070.0498-0.05150.296-0.1108-0.29830.04540.112-0.00270.01520.1264-0.02120.1485-23.37467.911617.0036
31.26710.65990.412.38431.19672.7281-0.0230.0882-0.17-0.01130.1698-0.14820.12530.4335-0.03020.107-0.00620.00420.1805-0.01530.1604-12.04770.721912.2271
45.7235-0.3771-0.9943.58091.26963.7273-0.04110.1471-0.16220.04060.0473-0.10180.08940.0871-0.01290.1021-0.00480.00420.09220.01370.1023-16.81390.698116.9117
54.6262.19380.35322.60881.56123.74010.02230.14-0.2159-0.00560.098-0.01020.14470.3891-0.03530.148-0.01460.00070.1408-0.01040.1447-18.0127-3.51935.8225
61.92640.2138-1.64310.2993-0.3741.1314-0.10860.21640.3603-0.09170.2535-0.13290.4325-0.0625-0.13980.2724-0.1407-0.03030.35310.03050.22461.265716.75229.1212
71.4181.1614-0.70831.68740.09540.87880.00910.0892-0.29030.35050.104-0.49040.24340.43980.10350.28740.0305-0.08820.40260.06150.282-4.98033.120424.7007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 18 )B2 - 18
2X-RAY DIFFRACTION2chain 'B' and (resid 19 through 74 )B19 - 74
3X-RAY DIFFRACTION3chain 'B' and (resid 75 through 129 )B75 - 129
4X-RAY DIFFRACTION4chain 'B' and (resid 130 through 159 )B130 - 159
5X-RAY DIFFRACTION5chain 'B' and (resid 160 through 203 )B160 - 203
6X-RAY DIFFRACTION6chain 'B' and (resid 204 through 228 )B204 - 228
7X-RAY DIFFRACTION7chain 'D' and (resid -1 through 7 )D-1 - 7

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