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- PDB-7duv: Structure of Sulfolobus solfataricus SegB protein -

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Basic information

Entry
Database: PDB / ID: 7duv
TitleStructure of Sulfolobus solfataricus SegB protein
ComponentsSegB
KeywordsDNA BINDING PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 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 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 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SegB
B: SegB
C: SegB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6405
Polymers41,4483
Non-polymers1922
Water1,00956
1
A: SegB

A: SegB


Theoretical massNumber of molelcules
Total (without water)27,6322
Polymers27,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4610 Å2
ΔGint-51 kcal/mol
Surface area9200 Å2
MethodPISA
2
B: SegB
C: SegB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8244
Polymers27,6322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-83 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.773, 61.773, 171.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 37 through 38 and (name N...
21(chain B and ((resid 37 through 38 and (name N...
31(chain C and ((resid 37 through 38 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYS(chain A and ((resid 37 through 38 and (name N...AA37 - 3837 - 38
12LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
13LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
14LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
15LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
21LYSLYS(chain B and ((resid 37 through 38 and (name N...BB37 - 3837 - 38
22LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
23LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
24LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
25LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
31LYSLYS(chain C and ((resid 37 through 38 and (name N...CC37 - 3837 - 38
32ARGARG(chain C and ((resid 37 through 38 and (name N...CC35 - 10635 - 106
33ARGARG(chain C and ((resid 37 through 38 and (name N...CC35 - 10635 - 106
34ARGARG(chain C and ((resid 37 through 38 and (name N...CC35 - 10635 - 106

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Components

#1: Protein SegB


Mass: 13815.950 Da / Num. of mol.: 3
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: SSO0035 / Production host: Escherichia coli (E. coli) / References: UniProt: Q981B2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.993 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 5959 / % possible obs: 99.1 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.046 / Rrim(I) all: 0.164 / Χ2: 1.063 / Net I/σ(I): 6.4 / Num. measured all: 72822
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3110.51.125460.9620.3331.1711.00396.5
3.31-3.4511.50.875870.9540.2540.9081.10898.5
3.45-3.612.20.6065730.9640.1750.6321.074100
3.6-3.7912.40.4055830.980.1170.4221.05499.3
3.79-4.0312.40.2695740.9950.0770.2811.08199.7
4.03-4.3412.80.1855940.9970.0530.1931.06199.8
4.34-4.7813.20.1336020.9980.0380.1391.073100
4.78-5.4613.40.1256010.9990.0350.131.048100
5.46-6.87130.1176290.9960.0330.1221.058100
6.87-3010.90.03567010.0110.0371.05997.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→29.07 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3257 535 10.01 %
Rwork0.2803 4809 -
obs0.2849 5344 89.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.52 Å2 / Biso mean: 26.6217 Å2 / Biso min: 0.95 Å2
Refinement stepCycle: final / Resolution: 3.2→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 10 56 1900
Biso mean--15.75 13.99 -
Num. residues----220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A489X-RAY DIFFRACTION1.232TORSIONAL
12B489X-RAY DIFFRACTION1.232TORSIONAL
13C489X-RAY DIFFRACTION1.232TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.520.31681080.3098968107675
3.52-4.030.31541310.26681179131090
4.03-5.070.31961420.25021279142195
5.08-29.070.34591540.30731383153797

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