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- PDB-6bhw: B. subtilis SsbA -

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Basic information

Entry
Database: PDB / ID: 6bhw
TitleB. subtilis SsbA
ComponentsSingle-stranded DNA-binding protein A
KeywordsDNA BINDING PROTEIN / Single-stranded DNA binding protein / DNA Replication / DNA Repair
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
DI(HYDROXYETHYL)ETHER / Single-stranded DNA-binding protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.208 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 1.4Oct 4, 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
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: Single-stranded DNA-binding protein A
F: Single-stranded DNA-binding protein A
G: Single-stranded DNA-binding protein A
H: Single-stranded DNA-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,06416
Polymers104,5248
Non-polymers5418
Water4,612256
1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6169
Polymers52,2624
Non-polymers3545
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-26 kcal/mol
Surface area21080 Å2
MethodPISA
2
E: Single-stranded DNA-binding protein A
F: Single-stranded DNA-binding protein A
G: Single-stranded DNA-binding protein A
H: Single-stranded DNA-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4487
Polymers52,2624
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-22 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.479, 97.479, 213.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 13065.486 Da / Num. of mol.: 8
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50% mixture with 50 mM MES pH6.5, 5% PEG 8000, 80 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-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52594 / % possible obs: 100 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.133 / Net I/σ(I): 36.4
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 15.5 % / Rmerge(I) obs: 1.32 / Num. unique obs: 2566 / CC1/2: 0.814 / Rrim(I) all: 1.366 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000v712data processing
PHENIX(1.12)refinement
Cootmodel building
PHENIX(1.12)phasing
HKL-2000v712data scaling
HKL-2000v712data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VDY

3vdy


Resolution: 2.208→42.713 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2583 2000 3.81 %
Rwork0.2316 --
obs0.2326 52493 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.208→42.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 35 256 6504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026455
X-RAY DIFFRACTIONf_angle_d0.4568763
X-RAY DIFFRACTIONf_dihedral_angle_d18.7973902
X-RAY DIFFRACTIONf_chiral_restr0.0451022
X-RAY DIFFRACTIONf_plane_restr0.0021156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.208-2.26320.29891390.28473501X-RAY DIFFRACTION99
2.2632-2.32440.32311410.28873556X-RAY DIFFRACTION100
2.3244-2.39280.32171390.27753547X-RAY DIFFRACTION100
2.3928-2.47010.29421410.27283542X-RAY DIFFRACTION100
2.4701-2.55830.31261420.26193571X-RAY DIFFRACTION100
2.5583-2.66070.31581400.2573544X-RAY DIFFRACTION100
2.6607-2.78180.28031420.2643577X-RAY DIFFRACTION100
2.7818-2.92840.33051410.26423587X-RAY DIFFRACTION100
2.9284-3.11190.30911430.24953589X-RAY DIFFRACTION100
3.1119-3.35210.30351440.24533634X-RAY DIFFRACTION100
3.3521-3.68920.23991420.21733588X-RAY DIFFRACTION100
3.6892-4.22260.22371450.20433669X-RAY DIFFRACTION100
4.2226-5.31850.1841470.17483695X-RAY DIFFRACTION100
5.3185-42.72140.23571540.23523893X-RAY DIFFRACTION100

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