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- PDB-7dv3: Structure of Sulfolobus solfataricus SegA-AMPPNP protein -

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Basic information

Entry
Database: PDB / ID: 7dv3
TitleStructure of Sulfolobus solfataricus SegA-AMPPNP protein
ComponentsSOJ protein (Soj)
KeywordsDNA BINDING PROTEIN / PARTITION PROTEIN
Function / homology: / AAA domain / AAA domain / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / SOJ protein (Soj)
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYen, C.Y. / Lin, M.G. / Wu, C.T. / 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 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

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Assembly

Deposited unit
A: SOJ protein (Soj)
B: SOJ protein (Soj)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7588
Polymers48,6492
Non-polymers1,1106
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-40 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.293, 62.058, 145.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SOJ protein (Soj)


Mass: 24324.348 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MES pH 6.0, Magnesium formate, Pentaerythritol ethoxylate (15/4 EO/OH)

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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: Oct 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 14837 / % possible obs: 95.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.048 / Rrim(I) all: 0.099 / Χ2: 0.95 / Net I/σ(I): 8.2 / Num. measured all: 59507
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.694.10.39814690.8540.2190.4570.93897.2
2.69-2.84.10.35214940.8960.1940.4050.9497.6
2.8-2.934.10.27614930.9340.1530.3180.99297.7
2.93-3.084.10.21214740.9540.1180.2441.02897.7
3.08-3.2840.15915030.9740.0880.1831.03897.7
3.28-3.5340.10114920.9910.0560.1161.01596.8
3.53-3.8840.07414850.9930.0410.0850.93796.1
3.88-4.443.90.05514740.9960.0310.0640.89894.6
4.44-5.593.90.04514620.9970.0250.0520.75492.7
5.59-303.90.04414910.9980.0250.0510.94388

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Processing

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

7dut


Resolution: 2.6→27.04 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 1403 9.99 %
Rwork0.2128 12635 -
obs0.2184 14038 90.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.27 Å2 / Biso mean: 45.1661 Å2 / Biso min: 22.77 Å2
Refinement stepCycle: final / Resolution: 2.6→27.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 66 22 3510
Biso mean--37.68 34.46 -
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.690.33471080.2662984109272
2.69-2.80.35671270.27611131125883
2.8-2.930.31761350.27711225136089
2.93-3.080.35491450.28551308145396
3.08-3.270.29731490.25391336148598
3.27-3.530.30851490.24591343149297
3.53-3.880.29341490.21771340148996
3.88-4.440.2321470.18291324147195
4.44-5.590.23441450.1721306145193
5.59-27.040.19411490.15841338148789

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