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- PDB-3eiv: Crystal Structure of Single-stranded DNA-binding protein from Str... -

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Basic information

Entry
Database: PDB / ID: 3eiv
TitleCrystal Structure of Single-stranded DNA-binding protein from Streptomyces coelicolor
ComponentsSingle-stranded DNA-binding protein 2
KeywordsDNA BINDING PROTEIN / Single-stranded DNA-binding protein / Streptomyces Coelicolor / DNA damage / DNA repair / DNA replication / DNA-binding / Phosphoprotein
Function / homology
Function and homology information


positive regulation of helicase activity / nucleoid / single-stranded DNA binding / DNA replication
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
Single-stranded DNA-binding protein 2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 2.141 Å
AuthorsLuic, M. / Stefanic, Z. / Vujaklija, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the single-stranded DNA-binding protein from Streptomyces coelicolor.
Authors: Stefanic, Z. / Vujaklija, D. / Luic, M.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2
C: Single-stranded DNA-binding protein 2
D: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)79,7024
Polymers79,7024
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-44 kcal/mol
Surface area20450 Å2
MethodPISA
2
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)39,8512
Polymers39,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-16 kcal/mol
Surface area11910 Å2
MethodPISA
3
C: Single-stranded DNA-binding protein 2
D: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)39,8512
Polymers39,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-14 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.454, 104.788, 163.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-213-

HOH

21B-259-

HOH

31C-294-

HOH

41D-217-

HOH

51D-231-

HOH

DetailsBiological unit is a tetramer. Biological unit is the same as asym. unit

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Components

#1: Protein
Single-stranded DNA-binding protein 2 / SSB 2 / Helix-destabilizing protein 2


Mass: 19925.531 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor (bacteria) / References: UniProt: Q9X8U3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM TRIS-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.14→32.2 Å / Num. all: 48150 / Num. obs: 31640 / % possible obs: 65.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.44 % / Biso Wilson estimate: 48.39 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.0739 / Net I/σ(I): 13.373
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / Num. measured all: 22946 / Num. unique all: 5720 / Rsym value: 0.41 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.2 Å
Translation2.5 Å32.2 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-3000data collection
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: PDB ENTRY 1X3E

1x3e


Resolution: 2.141→31.182 Å / FOM work R set: 0.772 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2437 5.07 %RANDOM
Rwork0.23 ---
obs0.232 27266 99.73 %-
all-44287 --
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.116 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 90.21 Å2 / Biso mean: 46.76 Å2 / Biso min: 24.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.461 Å20 Å2-0 Å2
2--12.193 Å20 Å2
3----14.655 Å2
Refinement stepCycle: LAST / Resolution: 2.141→31.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 288 3438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.915

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