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- PDB-4gs3: Dimeric structure of the N-terminal domain of PriB protein from T... -

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Basic information

Entry
Database: PDB / ID: 4gs3
TitleDimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tencongensis solved ab initio
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / primosome / oligonucleotide/oligosaccharide binding domain
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.09 Å
AuthorsLiebschner, D. / Brzezinski, K. / Dauter, M. / Dauter, Z. / Nowak, M. / Kur, J. / Olszewski, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio.
Authors: Liebschner, D. / Brzezinski, K. / Dauter, M. / Dauter, Z. / Nowak, M. / Kur, J. / Olszewski, M.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Refinement description
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Jan 23, 2013Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)12,2121
Polymers12,2121
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Single-stranded DNA-binding protein

A: Single-stranded DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)24,4242
Polymers24,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1830 Å2
ΔGint-6 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.560, 41.180, 38.780
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Single-stranded DNA-binding protein


Mass: 12211.942 Da / Num. of mol.: 1 / Fragment: UNP residues 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Ssb, TTE0829 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8RBI8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.81 Å3/Da / Density % sol: 32.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.14 M ammonium acetate, 0.07 M acetate buffer pH 4.6, 21% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→30 Å / Num. obs: 38376 / Redundancy: 4.1 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 29.3

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Processing

Software
NameClassification
HKL-3000data collection
SHELXDphasing
SHELXL-97refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.09→30 Å / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
all0.1544 --
obs0.1292 38376 -
Rfree-1830 5% random
Refinement stepCycle: LAST / Resolution: 1.09→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 0 96 833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d2.8

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