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- PDB-7dv2: Structure of Sulfolobus solfataricus SegB-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7dv2
TitleStructure of Sulfolobus solfataricus SegB-DNA complex
Components
  • DNA (5'-D(P*AP*CP*GP*TP*AP*GP*AP*AP*GP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*CP*TP*TP*CP*TP*AP*CP*GP*TP*A)-3')
  • SegB
KeywordsDNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA COMPLEX
Function / homologyDNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYen, C.Y. / Lin, M.G. / Sun, Y.J. / Hsiao, C.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.
Authors: Yen, C.Y. / Lin, M.G. / Chen, B.W. / Ng, I.W. / Read, N. / Kabli, A.F. / Wu, C.T. / Shen, Y.Y. / Chen, C.H. / Barilla, D. / Sun, Y.J. / Hsiao, C.D.
History
DepositionJan 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SegB
B: SegB
C: SegB
D: SegB
E: DNA (5'-D(P*AP*CP*GP*TP*AP*GP*AP*AP*GP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*G)-3')
F: DNA (5'-D(P*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*CP*TP*TP*CP*TP*AP*CP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)52,8606
Polymers52,8606
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-158 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.181, 121.785, 104.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
SegB


Mass: 9991.653 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal 33 residues truncated protein
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0035 / Production host: Escherichia coli (E. coli) / References: UniProt: Q981B2
#2: DNA chain DNA (5'-D(P*AP*CP*GP*TP*AP*GP*AP*AP*GP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*G)-3')


Mass: 6520.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: A21 missing / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*TP*CP*TP*TP*CP*TP*AP*CP*GP*TP*A)-3')


Mass: 6373.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium citrate tribasic dihydrate pH 5.0, magnesium chloride hexahydrate, PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 13274 / % possible obs: 98.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.045 / Rrim(I) all: 0.114 / Χ2: 0.851 / Net I/σ(I): 6.8 / Num. measured all: 83127
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.215.60.56512860.9630.2330.6130.73496.5
3.21-3.345.80.44912710.9630.1850.4860.81996.4
3.34-3.4960.35513060.9860.1460.3850.84897.7
3.49-3.676.20.26512880.9890.110.2880.88998
3.67-3.96.50.17913290.9960.0750.1950.86399.3
3.9-4.216.80.12413490.9970.0530.1360.899100
4.21-4.636.80.10413480.9970.0450.1140.90599.6
4.63-5.296.70.08213490.9970.0370.090.95899.7
5.29-6.666.60.05913630.9970.0270.0650.84299.8
6.66-305.50.03113850.9990.0160.0350.69496

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DUV

7duv


Resolution: 3.1→26.87 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 974 10 %
Rwork0.2291 8769 -
obs0.2337 9743 73.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.77 Å2 / Biso mean: 55.4415 Å2 / Biso min: 25.34 Å2
Refinement stepCycle: final / Resolution: 3.1→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 841 0 0 3338
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.260.3816800.323272080043
3.26-3.470.3605950.277785494951
3.47-3.730.31331120.27881018113061
3.73-4.110.26681390.23381242138174
4.11-4.70.26731640.22551498166289
4.7-5.910.27291910.2161714190599
5.91-26.870.24571930.20071723191697

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