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- PDB-1kaw: STRUCTURE OF SINGLE STRANDED DNA BINDING PROTEIN (SSB) -

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Basic information

Entry
Database: PDB / ID: 1kaw
TitleSTRUCTURE OF SINGLE STRANDED DNA BINDING PROTEIN (SSB)
ComponentsSINGLE-STRANDED DNA BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / SINGLE STRANDED DNA BINDING PROTEIN / SSB
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / SOS response / nucleoid / replisome / recombinational repair / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / DNA recombination ...single-stranded DNA-binding protein complex / SOS response / nucleoid / replisome / recombinational repair / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / 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
Single-stranded DNA-binding protein / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsRaghunathan, S. / Waksman, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl ...Title: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution.
Authors: Raghunathan, S. / Ricard, C.S. / Lohman, T.M. / Waksman, G.
History
DepositionDec 6, 1996Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
D: SINGLE-STRANDED DNA BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,9214
Polymers57,9214
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.080, 105.850, 90.240
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0301, -0.0368, -0.9989), (-0.0298, -0.9989, 0.0359), (-0.9991, 0.0287, -0.0312)40.5647, 79.5826, 38.5565
2given(0.2318, -0.0044, 0.9727), (-0.0257, -0.9997, 0.0016), (0.9724, -0.0253, -0.2319)-13.0048, 101.9584, 18.322

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Components

#1: Protein
SINGLE-STRANDED DNA BINDING PROTEIN / SSB


Mass: 14480.156 Da / Num. of mol.: 4 / Fragment: CHYMOTRYPTIC FRAGMENT, RESIDUES 1 - 135 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02339, UniProt: P0AGE0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.36 Å3/Da / Density % sol: 52 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
25 %(w/v)PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionNum. obs: 14346 / % possible obs: 89.7 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. obs: 12833 / % possible obs: 83.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementResolution: 2.9→8 Å / σ(F): 1
Details: MOLECULAR DYNAMICS RESTRAINED REFINEMENT FOLLOWED BY LEAST-SQUARES OPTIMIZATION
RfactorNum. reflection
Rfree0.289 -
Rwork0.221 -
obs0.221 10473
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 0 0 35 3079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg20
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å

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