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- PDB-8wq8: Structure of Saccharolobus solfataricus SegC (SSO0033) protein -

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Basic information

Entry
Database: PDB / ID: 8wq8
TitleStructure of Saccharolobus solfataricus SegC (SSO0033) protein
ComponentsSegC
KeywordsUNKNOWN FUNCTION / DNA BINDING PROTEIN / PARTITION PROTEIN
Function / homologynucleotide binding / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYen, C.Y. / Lin, M.G. / Sun, Y.J. / Hsiao, C.D.
Funding support Taiwan, 5items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
National Science Council (NSC, Taiwan)NSTC 111-2311-B-001-001 Taiwan
National Science Council (NSC, Taiwan)NSTC 111-2311-B-001-002 Taiwan
National Science Council (NSC, Taiwan)NSTC 110-2326-B-007-002 Taiwan
National Science Council (NSC, Taiwan)NSTC 111-2326-B-007-001 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea.
Authors: Lin, M.G. / Yen, C.Y. / Shen, Y.Y. / Huang, Y.S. / Ng, I.W. / Barilla, D. / Sun, Y.J. / Hsiao, C.D.
History
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SegC
B: SegC
C: SegC
D: SegC


Theoretical massNumber of molelcules
Total (without water)79,5814
Polymers79,5814
Non-polymers00
Water3,171176
1
A: SegC
B: SegC


Theoretical massNumber of molelcules
Total (without water)39,7912
Polymers39,7912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-15 kcal/mol
Surface area16000 Å2
MethodPISA
2
C: SegC
D: SegC


Theoretical massNumber of molelcules
Total (without water)39,7912
Polymers39,7912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-14 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.942, 156.942, 126.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
SegC


Mass: 19895.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Gene: SSO0033 / Production host: Escherichia coli (E. coli) / References: UniProt: Q981B4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.91 Å3/Da / Density % sol: 74.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl pH 8.5 and potassium thiocyanate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 39646 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Χ2: 0.92 / Net I/σ(I): 8.7 / Num. measured all: 253331
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.60.76738920.7850.9380.3210.8330.927100
2.9-3.026.60.5939140.8650.9630.2480.6410.942100
3.02-3.156.60.36838860.9410.9850.1540.40.954100
3.15-3.326.60.25739250.970.9920.1080.280.93699.9
3.32-3.536.50.18639240.9820.9950.0790.2030.955100
3.53-3.86.40.13239290.9880.9970.0560.1440.972100
3.8-4.186.30.09239420.9930.9980.0390.10.929100
4.18-4.786.20.06939870.9950.9990.030.0760.89499.9
4.78-6.026.30.06640400.9950.9990.0280.0720.876100
6.02-305.70.05542070.9950.9990.0250.0610.80799.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.43 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 2000 5.07 %
Rwork0.1815 --
obs0.1832 39461 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 0 176 5456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095372
X-RAY DIFFRACTIONf_angle_d0.9827200
X-RAY DIFFRACTIONf_dihedral_angle_d5.479732
X-RAY DIFFRACTIONf_chiral_restr0.06796
X-RAY DIFFRACTIONf_plane_restr0.008896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.38351390.28712620X-RAY DIFFRACTION99
2.87-2.950.30991410.27722613X-RAY DIFFRACTION99
2.95-3.030.33481390.25262629X-RAY DIFFRACTION99
3.03-3.130.29421410.24552625X-RAY DIFFRACTION99
3.13-3.240.26071410.24032649X-RAY DIFFRACTION100
3.24-3.370.27341410.21852643X-RAY DIFFRACTION100
3.37-3.520.24011420.1932662X-RAY DIFFRACTION100
3.53-3.710.20711410.17482649X-RAY DIFFRACTION100
3.71-3.940.21871430.16362668X-RAY DIFFRACTION100
3.94-4.250.21611440.15542686X-RAY DIFFRACTION100
4.25-4.670.1771430.14012698X-RAY DIFFRACTION100
4.67-5.340.17071450.14492712X-RAY DIFFRACTION100
5.35-6.720.22681460.19712745X-RAY DIFFRACTION100
6.72-29.430.16081540.16812862X-RAY DIFFRACTION99

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