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- PDB-2ihe: Crystal structure of wild-type single-stranded DNA binding protei... -

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Basic information

Entry
Database: PDB / ID: 2ihe
TitleCrystal structure of wild-type single-stranded DNA binding protein from Thermus aquaticus
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / Single-stranded DNA binding protein (SSB) / Thermophile organism / Protein-DNA interaction / Protein-protein interaction
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair
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
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFedorov, R. / Witte, G. / Urbanke, C. / Manstein, D.J. / Curth, U.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: 3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins.
Authors: Fedorov, R. / Witte, G. / Urbanke, C. / Manstein, D.J. / Curth, U.
History
DepositionSep 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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


Theoretical massNumber of molelcules
Total (without water)30,0691
Polymers30,0691
Non-polymers00
Water3,297183
1
A: Single-stranded DNA-binding protein

A: Single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)60,1372
Polymers60,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2840 Å2
ΔGint-18 kcal/mol
Surface area22400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.840, 80.670, 56.510
Angle α, β, γ (deg.)90.00, 124.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1074-

HOH

21A-1149-

HOH

DetailsThe biological assembly is created by applying the operation (-x, y, -z) with a shift: -1 0 -1

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Components

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


Mass: 30068.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: ssb / Plasmid: pETTaqSSB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9KH06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293.15 K / pH: 7.4
Details: 100 mM Imidazole, 35% 2-Ethoxyethanol, 200 mM Calcium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K, pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2004 / Details: MICROBEAM OPTICS
RadiationMonochromator: LIQUID N2 COOLED SI-111 DOUBLE CRYSTAL OR SI-111 CHANNEL CUT MONOCHROMATORS IN SERIES
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14759 / % possible obs: 96.8 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.427 / % possible all: 95.9

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Processing

Software
NameVersionClassification
ProDCdata collection
AMoREphasing
CNS1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SE8

1se8


Resolution: 2.1→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 753 -RANDOM
Rwork0.209 ---
obs0.209 14759 100 %-
all-14759 --
Displacement parametersBiso mean: 48.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 0 183 1830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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

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