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- PDB-8tfu: Structure of Red beta C-terminal domain in complex with SSB C-ter... -

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Basic information

Entry
Database: PDB / ID: 8tfu
TitleStructure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1
Components
  • Plasmid-derived single-stranded DNA-binding protein
  • Recombination protein bet
KeywordsDNA BINDING PROTEIN / Recombination / Recombineering / Single Strand Annealing / Single-stranded DNA binding protein / genome engineering
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / DNA binding
Similarity search - Function
Bacteriophage lambda, Recombination protein bet / RecT family / RecT family / 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
Recombination protein bet / Plasmid-derived single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å
AuthorsBell, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-2212951 United States
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Basis for the Interaction of Red beta Single-Strand Annealing Protein with Escherichia coli Single-Stranded DNA-Binding Protein.
Authors: Zakharova, K. / Liu, M. / Greenwald, J.R. / Caldwell, B.C. / Qi, Z. / Wysocki, V.H. / Bell, C.E.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recombination protein bet
B: Recombination protein bet
C: Plasmid-derived single-stranded DNA-binding protein
D: Plasmid-derived single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)21,4584
Polymers21,4584
Non-polymers00
Water2,684149
1
A: Recombination protein bet
D: Plasmid-derived single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,7292
Polymers10,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area5370 Å2
MethodPISA
2
B: Recombination protein bet
C: Plasmid-derived single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,7292
Polymers10,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.810, 68.252, 70.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Recombination protein bet


Mass: 9428.625 Da / Num. of mol.: 2 / Mutation: GSHM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: bet, betA, red-beta, redB / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P03698
#2: Protein/peptide Plasmid-derived single-stranded DNA-binding protein / SSB / Helix-destabilizing protein


Mass: 1300.392 Da / Num. of mol.: 2 / Fragment: C-terminal peptide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P28044
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.48 M sodium phosphate monobasic monohydrate, 1.2 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.48→35.444 Å / Num. obs: 25018 / % possible obs: 80.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.1
Reflection shellResolution: 1.48→1.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1251 / CC1/2: 0.409 / Rpim(I) all: 0.526 / Rrim(I) all: 1.33 / % possible all: 21.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPROC1.1.7data reduction
Aimless0.7.4data scaling
MOLREP11.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.482→34.149 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.003 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2202 1215 4.857 %
Rwork0.1815 23802 -
all0.183 --
obs-25017 80.106 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.246 Å2-0 Å2-0 Å2
2--0.141 Å2-0 Å2
3----0.387 Å2
Refinement stepCycle: LAST / Resolution: 1.482→34.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 149 1407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121276
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161211
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6311732
X-RAY DIFFRACTIONr_angle_other_deg0.5311.5882792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.56355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65310225
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.3431063
X-RAY DIFFRACTIONr_chiral_restr0.0790.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
X-RAY DIFFRACTIONr_nbd_refined0.2180.2279
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.21109
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2663
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2724
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.295
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.28
X-RAY DIFFRACTIONr_nbd_other0.2010.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.210
X-RAY DIFFRACTIONr_mcbond_it3.032.965632
X-RAY DIFFRACTIONr_mcbond_other3.0242.964632
X-RAY DIFFRACTIONr_mcangle_it4.3635.269783
X-RAY DIFFRACTIONr_mcangle_other4.3655.271784
X-RAY DIFFRACTIONr_scbond_it4.9353.55644
X-RAY DIFFRACTIONr_scbond_other4.9313.549645
X-RAY DIFFRACTIONr_scangle_it7.7516.293949
X-RAY DIFFRACTIONr_scangle_other7.7476.292950
X-RAY DIFFRACTIONr_lrange_it9.06534.2611506
X-RAY DIFFRACTIONr_lrange_other9.07532.0451474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.482-1.520.54820.48890.48122670.9870.9054.01410.474
1.52-1.5620.391310.425080.41822070.9240.90824.42230.414
1.562-1.6070.313360.379650.36821450.9380.91746.66670.363
1.607-1.6560.373710.33214460.33421050.9170.93472.06650.321
1.656-1.710.3791050.31917100.32320350.9170.93989.18920.303
1.71-1.770.285920.30717740.30519500.9480.94695.69230.277
1.77-1.8370.371110.28417500.28819020.9370.95397.84440.243
1.837-1.9120.259980.24417520.24518540.9550.96499.78420.199
1.912-1.9960.245670.20717020.20917700.9550.97299.94350.18
1.996-2.0930.207680.18914930.1916700.9690.97993.47310.173
2.093-2.2060.228740.17215050.17416100.9680.98498.07450.159
2.206-2.3390.181670.17813880.17815320.980.98294.97390.168
2.339-2.50.218820.16813480.17114350.9710.98399.65160.166
2.5-2.6990.23610.16512920.16813610.9680.98499.41220.17
2.699-2.9550.207420.16911820.1712370.9720.98298.94910.179
2.955-3.3010.249590.17410700.17711350.9570.9899.47140.194
3.301-3.8050.195470.1499640.15110180.9780.98699.31240.179
3.805-4.6460.204390.1348190.1378700.9790.98998.62070.167
4.646-6.5110.214370.1776530.1796960.9740.98399.13790.238
6.511-34.1490.138260.193920.1864290.990.97897.43590.279

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