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- PDB-7x8c: Crystal structure of a KTSC family protein from Euryarchaeon Meth... -

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Basic information

Entry
Database: PDB / ID: 7x8c
TitleCrystal structure of a KTSC family protein from Euryarchaeon Methanolobus vulcani
ComponentsKTSC domain-containing protein
KeywordsDNA BINDING PROTEIN / ARCHAEA / KTSC DOMAIN-CONTAINING PROTEIN / SINGLE-STRANDED
Function / homologyKTSC domain / KTSC domain / KTSC domain-containing protein
Function and homology information
Biological speciesMethanolobus vulcani (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsZhang, Z.F. / Zhu, K.L. / Chen, Y.Y. / Cao, P. / Gong, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170050 China
National Natural Science Foundation of China (NSFC)92051109 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Biochemical and structural characterization of a KTSC family single-stranded DNA-binding protein from Euryarchaea.
Authors: Tian, L. / Zhu, K. / Chen, Y. / Zheng, X. / Zhang, H. / Geng, Z. / Li, W. / Ding, N. / Chen, J. / Dong, Y. / Cao, P. / Gong, Y. / Zhang, Z.
History
DepositionMar 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: KTSC domain-containing protein
B: KTSC domain-containing protein
C: KTSC domain-containing protein
D: KTSC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7507
Polymers32,6814
Non-polymers693
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-31 kcal/mol
Surface area15030 Å2
Unit cell
Length a, b, c (Å)42.929, 66.763, 87.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
KTSC domain-containing protein


Mass: 8170.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanolobus vulcani (archaea) / Gene: SAMN04488589_2454 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A7Z7AYG0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M SUCCINATE-PHOSPHATE-GLYCINE BUFFER (PH8.5) AND 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 7166 / % possible obs: 99.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 38.19 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 7.5
Reflection shellResolution: 2.73→2.8 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 503

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RGI

4rgi


Resolution: 2.73→50 Å / SU ML: 0.4096 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 28.4258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278 361 5.06 %
Rwork0.219 6771 -
obs0.222 7132 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.13 Å2
Refinement stepCycle: LAST / Resolution: 2.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 3 84 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372320
X-RAY DIFFRACTIONf_angle_d0.83713100
X-RAY DIFFRACTIONf_chiral_restr0.0559318
X-RAY DIFFRACTIONf_plane_restr0.0049394
X-RAY DIFFRACTIONf_dihedral_angle_d22.0605908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-3.120.34691260.26492183X-RAY DIFFRACTION99.44
3.12-3.930.28151220.21042244X-RAY DIFFRACTION100
3.93-500.24471130.20732344X-RAY DIFFRACTION99.92

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