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- PDB-6irq: Complexed crystal structure of PaSSB with ssDNA dT25 at 1.91 angs... -

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Basic information

Entry
Database: PDB / ID: 6irq
TitleComplexed crystal structure of PaSSB with ssDNA dT25 at 1.91 angstrom resolution
Components
  • DNA (25-MER)
  • Single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN/DNA / single-strand DNA binding protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 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
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: Rsc Adv / Year: 2019
Title: Characterization of an SSB-dT25 complex: structural insights into the S-shaped ssDNA binding conformation.
Authors: Huang, Y.H. / Chen, I.C. / Huang, C.Y.
History
DepositionNov 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 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
B: Single-stranded DNA-binding protein
C: Single-stranded DNA-binding protein
D: Single-stranded DNA-binding protein
E: DNA (25-MER)
F: DNA (25-MER)


Theoretical massNumber of molelcules
Total (without water)70,2176
Polymers70,2176
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-49 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.488, 60.488, 131.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 13774.341 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ssb, PA4232 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P40947
#2: DNA chain DNA (25-MER)


Mass: 7559.863 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.: 115 / 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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG400, 100mM MES Sodium salt pH6.5, 100mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. obs: 40690 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.23
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.6 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYG

1eyg


Resolution: 1.91→29.472 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.246 2044 5.03 %
Rwork0.213 --
obs0.2147 40647 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→29.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 520 0 115 3881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083842
X-RAY DIFFRACTIONf_angle_d0.8745270
X-RAY DIFFRACTIONf_dihedral_angle_d15.6882148
X-RAY DIFFRACTIONf_chiral_restr0.065585
X-RAY DIFFRACTIONf_plane_restr0.005605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9092-1.95360.28431380.26532617X-RAY DIFFRACTION97
1.9536-2.00240.26951340.24012515X-RAY DIFFRACTION97
2.0024-2.05660.28121540.22982550X-RAY DIFFRACTION97
2.0566-2.11710.30261340.23172525X-RAY DIFFRACTION97
2.1171-2.18540.29061390.23222573X-RAY DIFFRACTION96
2.1854-2.26350.27321430.22452554X-RAY DIFFRACTION97
2.2635-2.35410.26671410.21692534X-RAY DIFFRACTION96
2.3541-2.46110.2711210.22962554X-RAY DIFFRACTION97
2.4611-2.59080.2721210.23742580X-RAY DIFFRACTION97
2.5908-2.7530.29061350.23932579X-RAY DIFFRACTION96
2.753-2.96540.29051440.23832513X-RAY DIFFRACTION97
2.9654-3.26350.24651190.22592626X-RAY DIFFRACTION98
3.2635-3.73490.23491410.19762624X-RAY DIFFRACTION99
3.7349-4.70250.18611420.18622646X-RAY DIFFRACTION100
4.7025-29.47590.24511380.20142613X-RAY DIFFRACTION99

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