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- PDB-6aep: Crystal structure of the ssDNA-binding domain of DnaT from Salmon... -

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Basic information

Entry
Database: PDB / ID: 6aep
TitleCrystal structure of the ssDNA-binding domain of DnaT from Salmonella enterica Serovar Typhimurium LT2 at 1.84 angstrom resolution
ComponentsPrimosomal protein 1
KeywordsDNA BINDING PROTEIN / Primosome / replication restart / DnaT / DNA binding
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1180 / Primosomal protein 1 / DnaT, DNA-binding domain / DnaT DNA-binding domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Primosomal protein 1
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: To Be Published
Title: Crystal structure of the ssDNA-binding domain of DnaT from Salmonella enterica Serovar Typhimurium LT2 at 1.84 angstrom resolution
Authors: Huang, Y.H. / Huang, C.Y.
History
DepositionAug 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Primosomal protein 1
B: Primosomal protein 1


Theoretical massNumber of molelcules
Total (without water)23,2922
Polymers23,2922
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.282, 93.526, 68.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Primosomal protein 1 / Primosomal protein I


Mass: 11646.032 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: dnaT, STM4544 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67524
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M Magnesium Sulfate, 100 mM MES Sodium Salt pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 15843 / % possible obs: 97.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.33 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.035 / Net I/σ(I): 28.12
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 4.08 / Num. unique obs: 1479 / Rsym value: 0.213 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OU6

4ou6


Resolution: 1.844→27.737 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.82
RfactorNum. reflection% reflection
Rfree0.2485 806 5.09 %
Rwork0.2154 --
obs0.2172 15826 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.844→27.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 106 1325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061258
X-RAY DIFFRACTIONf_angle_d0.7891709
X-RAY DIFFRACTIONf_dihedral_angle_d11.761733
X-RAY DIFFRACTIONf_chiral_restr0.044169
X-RAY DIFFRACTIONf_plane_restr0.006223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8441-1.95960.34961360.26932340X-RAY DIFFRACTION92
1.9596-2.11090.32081230.24622469X-RAY DIFFRACTION98
2.1109-2.32320.26531320.22152483X-RAY DIFFRACTION97
2.3232-2.65910.25081330.23232526X-RAY DIFFRACTION98
2.6591-3.34930.24831240.22962572X-RAY DIFFRACTION99
3.3493-27.73980.22861580.19352630X-RAY DIFFRACTION98

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