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- PDB-6bhx: B. subtilis SsbA with DNA -

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Basic information

Entry
Database: PDB / ID: 6bhx
TitleB. subtilis SsbA with DNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Single-stranded DNA-binding protein A
KeywordsDNA binding protein/DNA / Single-stranded DNA binding protein / DNA Replication / DNA Repair / DNA binding protein-DNA complex
Function / homology
Function and homology information


positive regulation of helicase activity / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Single-stranded DNA-binding protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.936 Å
AuthorsDubiel, K.D. / Myers, A.R. / Satyshur, K.A. / Keck, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098885 United States
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins.
Authors: Dubiel, K. / Myers, A.R. / Kozlov, A.G. / Yang, O. / Zhang, J. / Ha, T. / Lohman, T.M. / Keck, J.L.
History
DepositionOct 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Single-stranded DNA-binding protein A
B: Single-stranded DNA-binding protein A
C: Single-stranded DNA-binding protein A
D: Single-stranded DNA-binding protein A
E: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)67,4505
Polymers67,4505
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-55 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.939, 93.681, 100.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14592.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ssbA, BSU40900 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P37455
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 9080.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50% mixture with 50 mM MES pH 6.5, 7% PEG 8000, 100 mM magnesium acetate, 200 mM potassium chloride SsbA was incubated with a 1:2 SsbA to dT35 ratio and a-chymotrypsin prior to crystallization
PH range: 6.5 - 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 12270 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 14.48
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 597 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX(1.12)refinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.936→44.284 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.22
RfactorNum. reflection% reflection
Rfree0.2688 586 4.79 %
Rwork0.2163 --
obs0.2188 12228 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.936→44.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 220 0 31 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023358
X-RAY DIFFRACTIONf_angle_d0.4874584
X-RAY DIFFRACTIONf_dihedral_angle_d17.3121961
X-RAY DIFFRACTIONf_chiral_restr0.043533
X-RAY DIFFRACTIONf_plane_restr0.003564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9356-3.23090.3681540.28132842X-RAY DIFFRACTION100
3.2309-3.69830.28821530.22812839X-RAY DIFFRACTION100
3.6983-4.65860.24151490.18342910X-RAY DIFFRACTION100
4.6586-44.28890.23211300.21243051X-RAY DIFFRACTION100

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