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- PDB-7dut: Structure of Sulfolobus solfataricus SegA protein -

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Basic information

Entry
Database: PDB / ID: 7dut
TitleStructure of Sulfolobus solfataricus SegA 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 / ADENOSINE-5'-DIPHOSPHATE / SOJ protein (Soj)
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 11, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7763
Polymers24,3241
Non-polymers4522
Water2,018112
1
A: SOJ protein (Soj)
hetero molecules

A: 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
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)50.481, 142.947, 65.251
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 SOJ protein (Soj)


Mass: 24324.348 Da / Num. of mol.: 1
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293.15 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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 14301 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Rrim(I) all: 0.105 / Χ2: 0.929 / Net I/σ(I): 7.8 / Num. measured all: 98183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.147.10.6316940.940.2530.680.826100
2.14-2.187.20.557110.9410.220.5930.8599.9
2.18-2.227.30.5066940.950.2020.5450.903100
2.22-2.267.20.4256940.9670.170.4580.943100
2.26-2.317.30.3917200.9640.1550.4210.922100
2.31-2.377.20.3456830.9720.1370.3710.966100
2.37-2.427.20.3017140.9760.1210.3250.949100
2.42-2.497.20.2617070.9790.1050.2820.978100
2.49-2.567.20.237150.9840.0930.2490.989100
2.56-2.657.20.27050.9880.0810.2160.998100
2.65-2.747.10.1767140.9870.0710.190.983100
2.74-2.857.10.157090.9910.0610.1620.962100
2.85-2.987.10.1127040.9950.0460.1210.882100
2.98-3.1470.0927190.9960.0380.0990.90599.9
3.14-3.336.80.0827160.9950.0340.0890.952100
3.33-3.596.50.0697230.9970.030.0751.06100
3.59-3.956.30.0547120.9980.0240.0591.006100
3.95-4.526.10.0457380.9980.020.0490.88199.9
4.52-5.6960.047360.9980.0180.0440.84299.9
5.69-305.40.0387930.9980.0180.0420.75699.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IUB

6iub


Resolution: 2.1→26.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1375 10.01 %RANDOM
Rwork0.1897 12368 --
obs0.194 13743 96.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.33 Å2 / Biso mean: 29.2957 Å2 / Biso min: 10.06 Å2
Refinement stepCycle: final / Resolution: 2.1→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 28 112 1851
Biso mean--23.11 37.91 -
Num. residues----220
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 (%)
2.1-2.180.26951090.2318976108578
2.18-2.260.27911270.20831146127392
2.26-2.370.28921390.21431251139099
2.37-2.490.26961400.211712521392100
2.49-2.650.25311400.202412601400100
2.65-2.850.24111410.207712751416100
2.85-3.140.22211400.185512621402100
3.14-3.590.25051450.184412951440100
3.59-4.520.18741420.164712901432100
4.52-26.910.21481520.181913611513100

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