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- PDB-7dwr: Structure of Sulfolobus solfataricus SegA-ADP complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 7dwr
TitleStructure of Sulfolobus solfataricus SegA-ADP complex bound to DNA
Components
  • DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
  • SOJ protein (Soj)
KeywordsDNA BINDING PROTEIN / PARTITION PROTEIN / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / SOJ protein (Soj)
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYen, C.Y. / Lin, M.G. / Hsiao, C.D. / Sun, Y.J.
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 17, 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: SOJ protein (Soj)
B: SOJ protein (Soj)
C: SOJ protein (Soj)
D: SOJ protein (Soj)
E: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
G: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
H: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,58416
Polymers126,7788
Non-polymers1,8068
Water41423
1
A: SOJ protein (Soj)
C: SOJ protein (Soj)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5526
Polymers48,6492
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SOJ protein (Soj)
D: SOJ protein (Soj)
E: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
G: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
H: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
hetero molecules

E: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
G: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
H: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)108,51414
Polymers107,61110
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)220.000, 60.541, 132.143
Angle α, β, γ (deg.)90.000, 127.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SOJ protein (Soj)


Mass: 24324.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: soj, SSO0034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q981B3

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')


Mass: 7483.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')


Mass: 7256.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 31 molecules

#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES sodium salt pH 6.5, PEG8000, calcium acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 32772 / % possible obs: 94.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.066 / Rrim(I) all: 0.127 / Χ2: 0.92 / Net I/σ(I): 6.9 / Num. measured all: 117429
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.40.4515950.8560.2810.5320.88792.4
2.85-2.93.50.42216220.9120.2570.4960.84595.7
2.9-2.963.70.43316600.8870.2580.5060.89997.5
2.96-3.023.80.37417440.9240.220.4360.88998.9
3.02-3.083.90.35617150.9410.2060.4130.89699.5
3.08-3.1540.31116890.9550.1770.3590.93398.7
3.15-3.2340.27916800.9630.1580.3210.95298.3
3.23-3.3240.24517080.9690.1390.2830.99898.4
3.32-3.4240.20116820.9760.1150.2321.04198.5
3.42-3.533.90.17116950.9780.0980.1981.09997.6
3.53-3.653.90.1616870.9770.0920.1851.06497.5
3.65-3.83.70.13216630.9870.0760.1531.04794.9
3.8-3.973.60.11316200.9830.0670.1321.00794.8
3.97-4.183.50.10215410.9850.0610.121.03989.2
4.18-4.443.20.0815410.9940.050.0950.96988.7
4.44-4.783.10.07314650.990.0480.0890.86483.2
4.78-5.263.10.0615170.9960.0390.0730.80687.8
5.26-6.023.10.05716400.990.0390.070.69791.9
6.02-7.563.10.04816410.9940.0330.0590.6392.3
7.56-3030.04316670.9950.0310.0530.54392

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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: 7DUT

7dut


Resolution: 2.8→27.68 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1987 6.61 %
Rwork0.2389 28086 -
obs0.2428 30073 86.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.75 Å2 / Biso mean: 58.5863 Å2 / Biso min: 19.06 Å2
Refinement stepCycle: final / Resolution: 2.8→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6844 1968 112 23 8947
Biso mean--44.92 32.81 -
Num. residues----976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.33611020.2581485158765
2.87-2.950.33811190.25281614173371
2.95-3.030.30971270.25361795192278
3.03-3.130.29641330.26361887202083
3.13-3.240.3371470.26452072221990
3.24-3.370.30891590.25452241240096
3.37-3.530.31721560.23552202235897
3.53-3.710.3031490.24052196234596
3.71-3.940.28511580.23382206236495
3.94-4.250.30071490.22822085223490
4.25-4.670.29171370.21361963210085
4.67-5.350.28061410.22532009215086
5.35-6.720.31181540.25922161231592
6.72-27.680.2631560.22922170232690

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