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- PDB-5odp: Salinibacter ruber Single-Strand Binding protein D17K D71K mutant -

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Basic information

Entry
Database: PDB / ID: 5odp
TitleSalinibacter ruber Single-Strand Binding protein D17K D71K mutant
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / Single-Strand Binding protein
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 / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesSalinibacter ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.535 Å
AuthorsPierechod, M. / Rothweiler, U.
Citation
Journal: To Be Published
Title: Salinibacter ruber Single-Strand Binding protein D17K D71K mutant
Authors: Pierechod, M. / Rothweiler, U.
#1: Journal: Patent / Year: 2018
Title: Single-strand binding protein
Authors: Pierechod, M. / Willassen, N.P. / Rothweiler, U.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_patent / _citation.title
Revision 1.3Jan 17, 2024Group: 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
G: Single-stranded DNA-binding protein
L: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
M: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
N: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
O: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
P: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)58,8447
Polymers58,8447
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.587, 102.587, 61.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 21929.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: D17K and D71K point mutations
Source: (gene. exp.) Salinibacter ruber (strain DSM 13855 / M31) (bacteria)
Gene: ssb, SRU_0523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2S565
#2: DNA chain
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2996.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: 75 synthetic poly T single stranded DNA / Source: (synth.) Salinibacter ruber (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 10k 9.9%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.535→50 Å / Num. obs: 11326 / % possible obs: 99.6 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rrim(I) all: 0.122 / Net I/σ(I): 17.59
Reflection shellResolution: 2.535→2.69 Å / Mean I/σ(I) obs: 2.19 / Num. unique obs: 1764 / CC1/2: 0.678 / Rrim(I) all: 1.244 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODN

5odn


Resolution: 2.535→46.911 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.47
RfactorNum. reflection% reflection
Rfree0.2537 567 5.01 %
Rwork0.2167 --
obs0.2186 11321 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.535→46.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 318 0 4 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031903
X-RAY DIFFRACTIONf_angle_d0.6572626
X-RAY DIFFRACTIONf_dihedral_angle_d19.671718
X-RAY DIFFRACTIONf_chiral_restr0.026300
X-RAY DIFFRACTIONf_plane_restr0.003288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5355-2.79060.31281380.2642614X-RAY DIFFRACTION99
2.7906-3.19430.30361380.24722632X-RAY DIFFRACTION100
3.1943-4.02410.23221420.20812688X-RAY DIFFRACTION100
4.0241-46.91890.24151490.20442820X-RAY DIFFRACTION100

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