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- PDB-7ym1: Structure of SsbA protein in complex with the anticancer drug 5-f... -

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Basic information

Entry
Database: PDB / ID: 7ym1
TitleStructure of SsbA protein in complex with the anticancer drug 5-fluorouracil
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / single-strand DNA binding protein
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
5-FLUOROURACIL / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus ED98 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsHuang, Y.H. / Yang, P.C. / Chiang, W.Y. / Lin, E.S. / Huang, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of DNA Replication Protein SsbA Complexed with the Anticancer Drug 5-Fluorouracil.
Authors: Su, H.H. / Huang, Y.H. / Lien, Y. / Yang, P.C. / Huang, C.Y.
History
DepositionJul 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5124
Polymers25,2902
Non-polymers2222
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-10 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.091, 88.091, 57.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Single-stranded DNA-binding protein / SSB


Mass: 12645.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus ED98 (bacteria)
Gene: ssb, ssb2, ssb_1, ssbA, A6762_01715, BN1321_80086, C7P97_01495, CSC87_00615, CV021_06850, DD547_00353, E3A28_06905, E3K14_01855, E4U00_06870, EDCC5055_00340, EP54_08250, EQ90_08535, G6Y24_ ...Gene: ssb, ssb2, ssb_1, ssbA, A6762_01715, BN1321_80086, C7P97_01495, CSC87_00615, CV021_06850, DD547_00353, E3A28_06905, E3K14_01855, E4U00_06870, EDCC5055_00340, EP54_08250, EQ90_08535, G6Y24_06705, GO782_08865, GO788_13850, GO793_13375, GO814_10580, GO941_16005, GO942_09280, GZ128_07070, GZ156_06265, HK402_02025, HMPREF3211_02451, HUW54_01845, NCTC10702_00704, NCTC5664_00336, NCTC7878_00400, NCTC7972_01579, QU38_04380, SA0759_00307, SA950122_00302, SAJPND4_00365, SAMEA70245418_01284
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0D1JHQ1
#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 16% PEG4000, 100mM Tris, pH8.5, 200mM MgCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. obs: 9854 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 31.6
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 7 % / Mean I/σ(I) obs: 8.2 / Num. unique obs: 964 / CC1/2: 0.974 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGT

5xgt


Resolution: 2.36→27.86 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 476 4.85 %
Rwork0.201 9336 -
obs0.2037 9812 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.37 Å2 / Biso mean: 33.4772 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 2.36→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 26 52 1670
Biso mean--40.93 32.98 -
Num. residues----201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.36-2.70.28131710.196330293200
2.7-3.40.2831560.211830693225
3.4-27.860.23521490.196932383387

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