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

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Basic information

Entry
Database: PDB / ID: 8wqn
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: 1.8 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 12, 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 23, 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


Theoretical massNumber of molelcules
Total (without water)19,8951
Polymers19,8951
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Biological assembly 1 assigned by authors and generated by PISA (software)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.910, 70.152, 71.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SegC


Mass: 19895.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal missing
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.: 127 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate pH 4.6, calcium chloride, and MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 15953 / % possible obs: 96.3 % / Redundancy: 4.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.038 / Rrim(I) all: 0.082 / Χ2: 0.909 / Net I/σ(I): 10.6 / Num. measured all: 66122
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.864.10.38716010.8660.9630.2080.4410.87598.8
1.86-1.944.10.28415880.9240.980.1520.3230.92698.3
1.94-2.034.10.21115810.9530.9880.1130.2410.97298.1
2.03-2.134.10.15115980.9750.9940.0810.1720.96597.6
2.13-2.274.10.11216090.9840.9960.0590.1270.98397.5
2.27-2.444.10.09115820.990.9970.0480.1040.9897.1
2.44-2.694.20.07215830.9920.9980.0380.0820.90996.2
2.69-3.084.20.06115990.9930.9980.0320.070.92795.8
3.08-3.884.20.04615900.9950.9990.0240.0520.78694.1
3.88-304.10.04316220.9960.9990.0230.0490.7790.4

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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: 1.8→28.1 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1575 10 %
Rwork0.1864 --
obs0.1897 15757 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 0 127 1375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071270
X-RAY DIFFRACTIONf_angle_d0.8691703
X-RAY DIFFRACTIONf_dihedral_angle_d5.149172
X-RAY DIFFRACTIONf_chiral_restr0.059188
X-RAY DIFFRACTIONf_plane_restr0.008212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.21721380.18761213X-RAY DIFFRACTION92
1.86-1.920.18811290.18421269X-RAY DIFFRACTION95
1.92-20.20371520.18471304X-RAY DIFFRACTION97
2-2.090.22781440.17691283X-RAY DIFFRACTION98
2.09-2.20.20041440.17281298X-RAY DIFFRACTION97
2.2-2.340.23791410.17781301X-RAY DIFFRACTION97
2.34-2.520.25141480.17961297X-RAY DIFFRACTION97
2.52-2.770.22371420.19111293X-RAY DIFFRACTION96
2.77-3.170.23261380.20251311X-RAY DIFFRACTION96
3.17-40.2121440.17921300X-RAY DIFFRACTION94
4-28.10.21351550.19491313X-RAY DIFFRACTION90

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