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- PDB-5odl: Single-stranded DNA-binding protein from bacteriophage Enc34 in c... -

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Basic information

Entry
Database: PDB / ID: 5odl
TitleSingle-stranded DNA-binding protein from bacteriophage Enc34 in complex with ssDNA
Components
  • oligo(T)
  • single-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / DNA replication / DUF2815 / SSB / OB fold
Function / homologyEnterobacter phage Enc34, ssDNA-binding protein / Enterobacter phage Enc34, ssDNA-binding protein / Nucleic acid-binding, OB-fold / DNA binding / metal ion binding / DNA / SsDNA-binding protein
Function and homology information
Biological speciesEnterobacter phage Enc34 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsCernooka, E. / Rumnieks, J. / Kazaks, A. / Tars, K.
CitationJournal: Sci Rep / Year: 2017
Title: Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34.
Authors: Cernooka, E. / Rumnieks, J. / Tars, K. / Kazaks, A.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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
D: oligo(T)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3127
Polymers22,9212
Non-polymers3915
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-19 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.489, 43.489, 179.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein single-stranded DNA-binding protein


Mass: 20228.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter phage Enc34 (virus) / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6WYG2
#2: DNA chain oligo(T)


Mass: 2692.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 30% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.56→59.6 Å / Num. obs: 27151 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Net I/σ(I): 9.5
Reflection shellResolution: 1.56→1.56 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3942 / CC1/2: 0.389 / Rpim(I) all: 0.344 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODK

5odk


Resolution: 1.56→37.66 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19148 1316 4.9 %RANDOM
Rwork0.14094 ---
obs0.14336 25751 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.285 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.56→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 164 25 137 1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191681
X-RAY DIFFRACTIONr_bond_other_d00.021548
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9062302
X-RAY DIFFRACTIONr_angle_other_deg3.50333638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50824.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25115291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4441510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211709
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02293
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7012.405723
X-RAY DIFFRACTIONr_mcbond_other2.7132.398722
X-RAY DIFFRACTIONr_mcangle_it3.6163.602906
X-RAY DIFFRACTIONr_mcangle_other3.6173.605907
X-RAY DIFFRACTIONr_scbond_it4.4653.342958
X-RAY DIFFRACTIONr_scbond_other4.4123.322954
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6614.8691386
X-RAY DIFFRACTIONr_long_range_B_refined6.30631.3351828
X-RAY DIFFRACTIONr_long_range_B_other6.30931.3351827
X-RAY DIFFRACTIONr_rigid_bond_restr8.68133229
X-RAY DIFFRACTIONr_sphericity_free28.433585
X-RAY DIFFRACTIONr_sphericity_bonded11.19453233
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 89 -
Rwork0.275 1906 -
obs--99.5 %

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