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- PDB-8tg7: Structure of Red beta C-terminal domain in complex with SSB C-ter... -

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Basic information

Entry
Database: PDB / ID: 8tg7
TitleStructure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 2
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


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: 1.775 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 12, 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
Water1,74797
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 area1070 Å2
ΔGint-9 kcal/mol
Surface area5100 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 area1030 Å2
ΔGint-9 kcal/mol
Surface area5180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.313, 69.222, 70.536
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: N-terminal GSHM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: bet, betA, red-beta, redB / 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 / Source method: obtained synthetically
Details: Peptide corresponding to the C-terminal nine residues of E. coli SSB protein, with N-terminal tryptophan
Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P28044
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 2.0 M ammonium sulfate, 0.1 M Tris pH 8.6

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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 / Details: KB mirrors, fixed focus
RadiationMonochromator: Kohzu HLD-15 Double Crystal cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.775→49.41 Å / Num. obs: 16243 / % possible obs: 86.5 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 1.775→1.891 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.399 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 812 / CC1/2: 0.659 / Rpim(I) all: 0.576 / Rrim(I) all: 1.516 / % possible all: 25.5

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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: 1.775→49.405 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.138 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2341 881 5.424 %
Rwork0.1816 15362 -
all0.184 --
obs-16243 86.45 %
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: 40.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2---0.081 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.775→49.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 0 97 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161182
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.6341682
X-RAY DIFFRACTIONr_angle_other_deg0.4881.592729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.46556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27210226
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.7261064
X-RAY DIFFRACTIONr_chiral_restr0.0730.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined0.2120.2277
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21063
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2640
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.26
X-RAY DIFFRACTIONr_nbd_other0.210.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.22
X-RAY DIFFRACTIONr_mcbond_it3.753.91604
X-RAY DIFFRACTIONr_mcbond_other3.7383.908604
X-RAY DIFFRACTIONr_mcangle_it4.8816.962748
X-RAY DIFFRACTIONr_mcangle_other4.8946.964749
X-RAY DIFFRACTIONr_scbond_it5.534.685638
X-RAY DIFFRACTIONr_scbond_other5.5264.683639
X-RAY DIFFRACTIONr_scangle_it8.6238.311934
X-RAY DIFFRACTIONr_scangle_other8.6188.31935
X-RAY DIFFRACTIONr_lrange_it9.57739.9291437
X-RAY DIFFRACTIONr_lrange_other9.57639.2141423
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
1.775-1.8210.412110.291160.313780.8780.9149.21630.281
1.821-1.8710.418210.2933860.313260.8720.93330.69380.29
1.871-1.9250.329450.3099330.3113050.9240.9374.94250.296
1.925-1.9840.304650.27511690.27712370.9330.94199.75750.261
1.984-2.0490.284940.24111250.24412200.9450.95999.9180.22
2.049-2.1210.324710.21711100.22311820.9260.96799.91540.195
2.121-2.20.23670.19610660.19811350.9640.97399.82380.17
2.2-2.290.225540.18510440.18710980.9710.9771000.159
2.29-2.3920.289580.17310060.17910660.9490.98199.81240.147
2.392-2.5080.162560.1639550.16310130.9810.98399.80260.14
2.508-2.6430.215530.1589120.1619660.9780.98499.89650.139
2.643-2.8030.364490.1738710.1819220.9310.98199.78310.154
2.803-2.9960.208350.1788280.1798650.9760.98199.76880.166
2.996-3.2350.221360.1737740.1758130.9760.98199.6310.167
3.235-3.5420.215350.1647140.1667520.9660.98499.60110.172
3.542-3.9580.255330.1666520.1716890.9630.98399.41940.182
3.958-4.5660.178280.1525690.1536040.980.98698.84110.176
4.566-5.580.177260.185070.1795340.9830.98299.81270.214
5.58-7.8410.312270.2293910.2354230.9450.96798.8180.274
7.841-49.4050.158170.1822340.182610.9820.97796.16860.269

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