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- PDB-7fex: Crystal structure of Sus scrofa Schlafen11 N-terminal domain (2.69 A) -

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Basic information

Entry
Database: PDB / ID: 7fex
TitleCrystal structure of Sus scrofa Schlafen11 N-terminal domain (2.69 A)
ComponentsSLFN11
KeywordsANTIVIRAL PROTEIN / Host antiviral protein / RNA helicase
Function / homology
Function and homology information


defense response to virus / tRNA binding / ATP binding
Similarity search - Function
Schlafen group 3-like, DNA/RNA helicase domain / Schlafen group 3, DNA/RNA helicase domain / Schlafen family / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Schlafen family member 11
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsHou, P. / Hao, W. / Cui, S.
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural and biochemical characterization of Schlafen11 N-terminal domain.
Authors: Hou, P. / Hao, W. / Qin, B. / Li, M. / Zhao, R. / Cui, S.
History
DepositionJul 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SLFN11


Theoretical massNumber of molelcules
Total (without water)38,8591
Polymers38,8591
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, No
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.991, 64.991, 344.018
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein SLFN11


Mass: 38858.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLFN11 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5G2RKN9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 22%PEG3350, 0.15M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.69→43.564 Å / Num. obs: 22498 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 34.4 % / Biso Wilson estimate: 61.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Net I/σ(I): 26.33
Reflection shellResolution: 2.69→2.71 Å / Redundancy: 34.8 % / Rmerge(I) obs: 1.15 / Num. unique obs: 3610 / CC1/2: 0.886 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69→43.56 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 695 5.42 %
Rwork0.2153 21278 -
obs0.2177 22498 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.51 Å2 / Biso mean: 66.8739 Å2 / Biso min: 36.12 Å2
Refinement stepCycle: final / Resolution: 2.69→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 0 10 2559
Biso mean---59.2 -
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.69-2.80.39321330.330823572490
2.8-2.930.35221110.304123962507
2.93-3.080.39611370.272423762513
3.08-3.280.25411470.242423372484
3.28-3.530.25041360.244823622498
3.53-3.880.26991280.204323832511
3.88-4.440.2151440.18123342478
4.45-5.590.21151290.17623762505
5.6-43.560.25881550.206123572512
Refinement TLS params.Method: refined / Origin x: 2.3292 Å / Origin y: 15.9678 Å / Origin z: -9.8295 Å
111213212223313233
T0.4969 Å20.07 Å2-0.1025 Å2-0.5312 Å2-0.1291 Å2--0.4018 Å2
L1.5399 °2-1.7761 °2-1.1668 °2-4.3456 °21.8438 °2--0.9919 °2
S-0.1237 Å °-0.0248 Å °0.0209 Å °0.3427 Å °-0.0094 Å °0.3586 Å °0.1781 Å °-0.0103 Å °0.121 Å °
Refinement TLS groupSelection details: Chain A

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