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- PDB-8gw5: Crystal structure of SaSsbA complexed with glycerol -

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Basic information

Entry
Database: PDB / ID: 8gw5
TitleCrystal structure of SaSsbA complexed with glycerol
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
Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus ED98 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYang, P.C. / Huang, H.Y. / 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
DepositionSep 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: 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

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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)25,7334
Polymers25,5492
Non-polymers1842
Water2,720151
1
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)51,4658
Polymers51,0974
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8860 Å2
ΔGint-45 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.224, 88.224, 57.999
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: 12774.273 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, CV021_06850, DD547_00353, E3A28_06905, E3K14_01855, E4U00_06870, EDCC5055_00340, EP54_08250, EQ90_08535, G6Y24_06705, GO782_ ...Gene: ssb, ssb2, ssb_1, ssbA, A6762_01715, BN1321_80086, C7P97_01495, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% PEG 4000, 100mM HEPES, pH7.5, 200mM CaCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 21823 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 35.7
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 100 / CC1/2: 0.955

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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: 1.8→27.9 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 1054 4.84 %
Rwork0.2035 20714 -
obs0.2049 21768 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.52 Å2 / Biso mean: 24.9766 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.8→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 28 151 1768
Biso mean--25.31 30.1 -
Num. residues----200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.880.31321200.248725492669
1.88-1.980.24391220.200225302652
1.98-2.10.18611480.180225392687
2.11-2.270.22461200.196225642684
2.27-2.50.24251240.210325732697
2.5-2.860.25421400.212425942734
2.86-3.60.24241440.201225952739
3.6-27.90.21621360.201427702906

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