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- PDB-1eyg: Crystal structure of chymotryptic fragment of E. coli ssb bound t... -

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Basic information

Entry
Database: PDB / ID: 1eyg
TitleCrystal structure of chymotryptic fragment of E. coli ssb bound to two 35-mer single strand DNAS
Components
  • SINGLE STRANDED 28-MER OF D(C)
  • SINGLE-STRAND DNA-BINDING PROTEIN
Keywordsreplication/DNA / PROTEIN-DNA COMPLEX / OB fold / Se-Met / MAD PHASING / SSB / binding mode / replication-DNA COMPLEX
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding ...single-stranded DNA-binding protein complex / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / identical protein binding / cytosol
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 / DNA (> 10) / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsRaghunathan, S. / Waksman, G.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the DNA binding domain of E. coli SSB bound to ssDNA.
Authors: Raghunathan, S. / Kozlov, A.G. / Lohman, T.M. / Waksman, G.
History
DepositionMay 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
Q: SINGLE STRANDED 28-MER OF D(C)
R: SINGLE STRANDED 28-MER OF D(C)
A: SINGLE-STRAND DNA-BINDING PROTEIN
B: SINGLE-STRAND DNA-BINDING PROTEIN
C: SINGLE-STRAND DNA-BINDING PROTEIN
D: SINGLE-STRAND DNA-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)71,7796
Polymers71,7796
Non-polymers00
Water70339
1
R: SINGLE STRANDED 28-MER OF D(C)
A: SINGLE-STRAND DNA-BINDING PROTEIN
B: SINGLE-STRAND DNA-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8903
Polymers35,8903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: SINGLE STRANDED 28-MER OF D(C)
C: SINGLE-STRAND DNA-BINDING PROTEIN
D: SINGLE-STRAND DNA-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,8903
Polymers35,8903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.688, 71.081, 79.160
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain SINGLE STRANDED 28-MER OF D(C)


Mass: 10076.405 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
SINGLE-STRAND DNA-BINDING PROTEIN / SSB-C


Mass: 12906.591 Da / Num. of mol.: 4 / Fragment: CHYMOTRYPTIC FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGE0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 7

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: PEG 4000,PEG 200, Hepes, pH 7.5, vapor diffusion, macro seeding, temperature 291K, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2PEG 20011
3PEG 400011
4PEG 20012
5PEG 400012
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
230 %(v/v)PEG2001reservoir
320 %(v/v)PEG40001reservoir
41
51

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9686
DetectorDetector: CCD / Date: Mar 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 13499 / Num. obs: 11228 / % possible obs: 82.5 % / Observed criterion σ(F): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.246
Reflection
*PLUS
Num. obs: 13271 / % possible obs: 97.6 % / Num. measured all: 44241 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.89 Å / % possible obs: 96.7 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.5refinement
RefinementResolution: 2.8→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 272185.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1204 9.7 %RANDOM
Rwork0.256 ---
obs0.256 12430 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.06 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.87 Å20 Å25.42 Å2
2--9.82 Å20 Å2
3----5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 960 0 39 4244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d30.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 144 8.4 %
Rwork0.307 1578 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PA
X-RAY DIFFRACTION3WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 9.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 51.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg30.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / % reflection Rfree: 8.4 % / Rfactor Rwork: 0.307

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