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- PDB-8yk9: Structure of Saccharolobus solfataricus SegC (SSO0033) protein, A... -

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Basic information

Entry
Database: PDB / ID: 8yk9
TitleStructure of Saccharolobus solfataricus SegC (SSO0033) protein, ATP soak
ComponentsSegC
KeywordsUNKNOWN FUNCTION / DNA BINDING PROTEIN / PARTITION PROTEIN
Function / homologynucleotide binding / metal ion binding / ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 111-2326-B-007-001 Taiwan
National Science Council (NSC, Taiwan)NSTC 110-2326-B-007-002 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
DepositionMar 4, 2024Deposition 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3159
Polymers79,5814
Non-polymers1,7335
Water00
1
A: SegC
B: SegC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6695
Polymers39,7912
Non-polymers8793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-34 kcal/mol
Surface area17100 Å2
MethodPISA
2
C: SegC
D: SegC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6454
Polymers39,7912
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-17 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.233, 159.233, 127.871
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: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / 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
Has ligand of interestY
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: 5.09 Å3/Da / Density % sol: 75.85 %
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 05A / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 23100 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Χ2: 0.939 / Net I/σ(I): 18.1 / Num. measured all: 145208
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.4-3.526.20.6422340.8290.9520.2830.7020.87399.9
3.52-3.666.60.38222860.9260.980.1620.4160.85100
3.66-3.836.70.2222670.9570.9890.0920.2390.975100
3.83-4.036.20.22922810.9780.9940.10.250.997100
4.03-4.286.60.1422720.9910.9980.0590.1530.944100
4.28-4.616.20.09622920.9950.9990.0410.1040.94399.7
4.61-5.076.50.08123100.9970.9990.0340.0880.95999.9
5.07-5.86.50.06923270.9970.9990.0290.0750.997100
5.8-7.2960.05923620.9970.9990.0260.0650.9999.8
7.29-305.50.03524690.9980.9990.0150.0390.85599.1

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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: 3.4→29.67 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1999 8.7 %
Rwork0.1972 --
obs0.1999 22971 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 109 0 5389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125488
X-RAY DIFFRACTIONf_angle_d1.3817380
X-RAY DIFFRACTIONf_dihedral_angle_d15.2776
X-RAY DIFFRACTIONf_chiral_restr0.069812
X-RAY DIFFRACTIONf_plane_restr0.014900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.480.42891330.37271384X-RAY DIFFRACTION94
3.48-3.580.33721410.27481485X-RAY DIFFRACTION100
3.58-3.680.29851410.28391483X-RAY DIFFRACTION100
3.68-3.80.31541410.2741481X-RAY DIFFRACTION100
3.8-3.940.24721410.23781476X-RAY DIFFRACTION100
3.94-4.10.30971420.24251486X-RAY DIFFRACTION99
4.1-4.280.23651410.19621479X-RAY DIFFRACTION100
4.28-4.510.22271420.18361483X-RAY DIFFRACTION99
4.51-4.790.19841420.17031496X-RAY DIFFRACTION99
4.79-5.160.19161430.16331506X-RAY DIFFRACTION100
5.16-5.670.22111450.17251516X-RAY DIFFRACTION100
5.67-6.480.24611450.21691520X-RAY DIFFRACTION100
6.49-8.140.25741490.18951554X-RAY DIFFRACTION100
8.15-29.670.15061530.14971623X-RAY DIFFRACTION99

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