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

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Basic information

Entry
Database: PDB / ID: 6aeq
TitleCrystal structure of the ssDNA-binding domain of DnaT from Salmonella enterica Serovar Typhimurium LT2
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
Replication restart protein DnaT
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2518084706 Å
AuthorsHuang, Y.H. / Huang, C.Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure of the C-terminal domain of the primosomal DnaT protein: Insights into a new oligomerization mechanism.
Authors: Chen, K.L. / Huang, Y.H. / Liao, J.F. / Lee, W.C. / Huang, C.Y.
History
DepositionAug 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-8 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.909, 92.319, 69.005
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 84 - 155 / Label seq-ID: 1 - 72

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22(chain 'B' and resid 84 through 155)BB

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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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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.: 16 / 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: 1.88 Å3/Da / Density % sol: 34.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Magnesium Sulfate, 100mM MES Sodium Salt pH 6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 8294 / % possible obs: 98.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.14
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.58 / Num. unique obs: 764 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OU6

4ou6


Resolution: 2.2518084706→21.48309024 Å / SU ML: 0.235716035848 / Cross valid method: THROUGHOUT / σ(F): 1.33784763378 / Phase error: 34.1707603168
RfactorNum. reflection% reflection
Rfree0.26517872003 448 5.41520609211 %
Rwork0.220106655196 --
obs0.222361580082 8273 96.3320912902 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.3122439788 Å2
Refinement stepCycle: LAST / Resolution: 2.2518084706→21.48309024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 16 1235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008853405784951258
X-RAY DIFFRACTIONf_angle_d1.212903094911709
X-RAY DIFFRACTIONf_chiral_restr0.0652712886822169
X-RAY DIFFRACTIONf_plane_restr0.00877873945111223
X-RAY DIFFRACTIONf_dihedral_angle_d14.1205627049733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2518-2.57720.3196579554851450.274936343252353X-RAY DIFFRACTION89.1506067095
2.5772-3.24520.3513223152911630.260790298412675X-RAY DIFFRACTION99.9295774648
3.2452-21.48410.2187225780851400.1963457881922797X-RAY DIFFRACTION99.6945010183

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