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- PDB-8d2m: Covalent Schiff base complex of YedK C2A and abasic DNA -

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Basic information

Entry
Database: PDB / ID: 8d2m
TitleCovalent Schiff base complex of YedK C2A and abasic DNA
Components
  • Abasic site processing protein YedK
  • DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA-protein crosslink / abasic site / Schiff base / replication stress / DNA BINDING PROTEIN / dna binding / protein-dna complex / 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 (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP)
Similarity search - Domain/homology
DNA / Abasic site processing protein YedK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.821 Å
AuthorsEichman, B.F. / Paulin, K.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136401 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES030575 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F31ES032334 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA-protein cross-link.
Authors: Paulin, K.A. / Cortez, D. / Eichman, B.F.
History
DepositionMay 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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
A: Abasic site processing protein YedK
C: DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')
B: Abasic site processing protein YedK
D: DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)55,2124
Polymers55,2124
Non-polymers00
Water2,882160
1
A: Abasic site processing protein YedK
C: DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,6062
Polymers27,6062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abasic site processing protein YedK
D: DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,6062
Polymers27,6062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.940, 41.473, 82.580
Angle α, β, γ (deg.)90.000, 95.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Abasic site processing protein YedK


Mass: 25574.828 Da / Num. of mol.: 2 / Mutation: C2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yedK / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P76318, Hydrolases; Acting on peptide bonds (peptidases)
#2: DNA chain DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')


Mass: 2031.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 25% (wt/vol) PEG 3350, 0.2 M sodium phosphate monobasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.82→37.03 Å / Num. obs: 37024 / % possible obs: 99.53 % / Redundancy: 2.1 % / Biso Wilson estimate: 19.8 Å2 / Rrim(I) all: 0.101 / Rsym value: 0.076 / Net I/av σ(I): 11.9 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.940.7636940.6490.4340.8771.03100
1.9-1.974.10.54636670.7980.310.631.08296.06
1.97-2.064.10.39836900.8750.2250.4581.163100
2.06-2.174.10.28236430.9290.1590.3251.255100
2.17-2.314.10.21937160.9590.1230.2521.347100
2.31-2.484.10.16336590.9740.0920.1871.307100
2.48-2.734.10.12337110.9860.0690.1411.241100
2.73-3.134.10.08336990.9920.0470.0961.166100
3.13-3.944.10.04837290.9970.0270.0551.064100
3.94-503.90.03438300.9980.0190.0391.01499.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.38 Å37.03 Å
Translation4.38 Å37.03 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NUA

6nua


Resolution: 1.821→37.025 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 1852 5 %
Rwork0.1777 35172 -
obs0.1802 37024 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.9 Å2 / Biso mean: 29.3513 Å2 / Biso min: 9.73 Å2
Refinement stepCycle: final / Resolution: 1.821→37.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 268 0 160 3928
Biso mean---27.84 -
Num. residues----460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8213-1.87060.3071350.2539256495
1.8706-1.92560.30991410.22212682100
1.9256-1.98780.25571430.21672707100
1.9878-2.05880.27511420.20852697100
2.0588-2.14120.24151400.18652675100
2.1412-2.23870.20961430.17752716100
2.2387-2.35670.2561420.1752700100
2.3567-2.50430.25081440.18132713100
2.5043-2.69760.241410.19742697100
2.6976-2.9690.25191450.19662735100
2.969-3.39840.23131430.18192735100
3.3984-4.28060.19261450.14772741100
4.2806-37.0250.1821480.1546281099

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