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- PDB-5odk: Single-stranded DNA-binding protein from bacteriophage Enc34, C-t... -

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Basic information

Entry
Database: PDB / ID: 5odk
TitleSingle-stranded DNA-binding protein from bacteriophage Enc34, C-terminal truncation
Componentssingle-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 / PHOSPHATE ION / SsDNA-binding protein
Function and homology information
Biological speciesEnterobacter phage Enc34 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9646
Polymers60,6843
Non-polymers2793
Water9,548530
1
A: single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5074
Polymers20,2281
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)20,2281
Polymers20,2281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)20,2281
Polymers20,2281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.770, 103.620, 59.290
Angle α, β, γ (deg.)90.00, 111.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein single-stranded DNA-binding protein


Mass: 20228.146 Da / Num. of mol.: 3
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.04 M potassium dihydrogen phosphate, 16% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97181 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97181 Å / Relative weight: 1
ReflectionResolution: 1.34→29.61 Å / Num. obs: 126056 / % possible obs: 99.3 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.032 / Net I/σ(I): 12.6
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 18326 / CC1/2: 0.814 / Rpim(I) all: 0.266 / % possible all: 99.1

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Processing

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

5odj


Resolution: 1.34→29.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18633 6157 4.9 %RANDOM
Rwork0.15044 ---
obs0.15215 119860 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.85 Å2
2---0.32 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.34→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 17 530 4679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194286
X-RAY DIFFRACTIONr_bond_other_d00.024099
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9895785
X-RAY DIFFRACTIONr_angle_other_deg3.57139613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78724.972179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73115821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3271521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214645
X-RAY DIFFRACTIONr_gen_planes_other0.010.02772
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_it1.9621.8342107
X-RAY DIFFRACTIONr_mcbond_other1.9511.8342106
X-RAY DIFFRACTIONr_mcangle_it2.4282.7612634
X-RAY DIFFRACTIONr_mcangle_other2.4312.7622635
X-RAY DIFFRACTIONr_scbond_it2.832.2872179
X-RAY DIFFRACTIONr_scbond_other2.8312.2872180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3873.2713148
X-RAY DIFFRACTIONr_long_range_B_refined4.03923.3074701
X-RAY DIFFRACTIONr_long_range_B_other3.97123.1694681
X-RAY DIFFRACTIONr_rigid_bond_restr12.72738385
X-RAY DIFFRACTIONr_sphericity_free25.2795366
X-RAY DIFFRACTIONr_sphericity_bonded10.57658456
LS refinement shellResolution: 1.343→1.378 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 437 -
Rwork0.241 8776 -
obs--98.25 %

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