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- PDB-7xwy: Crystal structure of spFft3 N-terminal truncation -

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Basic information

Entry
Database: PDB / ID: 7xwy
TitleCrystal structure of spFft3 N-terminal truncation
ComponentsATP-dependent helicase fft3
KeywordsDNA BINDING PROTEIN / DNA binding / remodeler / nucleosome / Fft3
Function / homology
Function and homology information


attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / histone chaperone activity / transcription elongation-coupled chromatin remodeling / replication fork processing / ATP-dependent activity, acting on DNA / heterochromatin / helicase activity / DNA helicase / damaged DNA binding ...attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / histone chaperone activity / transcription elongation-coupled chromatin remodeling / replication fork processing / ATP-dependent activity, acting on DNA / heterochromatin / helicase activity / DNA helicase / damaged DNA binding / chromatin remodeling / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
: / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal ...: / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent helicase fft3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsZhang, N. / Jiang, T. / Huo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800632 China
CitationJournal: To Be Published
Title: Crystal structure of spFft3 N-terminal truncation
Authors: Zhang, N. / Jiang, T. / Huo, Y.
History
DepositionMay 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent helicase fft3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1392
Polymers45,0431
Non-polymers961
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.716, 36.106, 101.973
Angle α, β, γ (deg.)90.000, 95.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent helicase fft3 / Fun thirty-related protein 3


Mass: 45042.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: fft3, snf2SR, SPAC25A8.01c / Production host: Escherichia coli (E. coli) / References: UniProt: O42861, DNA helicase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.14 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→38.132 Å / Num. obs: 33411 / % possible obs: 99.02 % / Redundancy: 6.6 % / CC1/2: 0.971 / Net I/σ(I): 9.2
Reflection shellResolution: 2.25→2.31 Å / Num. unique obs: 1220 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→38.132 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 3342 10 %
Rwork0.1828 30069 -
obs0.1882 33411 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.87 Å2 / Biso mean: 30.0479 Å2 / Biso min: 9.45 Å2
Refinement stepCycle: final / Resolution: 2.25→38.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 5 168 3209
Biso mean--28.59 32.36 -
Num. residues----381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2501-2.28220.29051160.2174101780
2.2822-2.31630.27591210.1993104182
2.3163-2.35250.34961290.2101119288
2.3525-2.3910.29081350.1993117191
2.391-2.43230.2841290.1975123793
2.4323-2.47650.31031340.2098120095
2.4765-2.52410.27511460.2056126195
2.5241-2.57560.25591450.2139127798
2.5756-2.63160.30461430.2017128298
2.6316-2.69280.27121460.2163127298
2.6928-2.76010.25411390.2072131399
2.7601-2.83470.28581390.2139125698
2.8347-2.91810.26071460.19841297100
2.9181-3.01230.23651460.20391333100
3.0123-3.11990.29671430.209127299
3.1199-3.24470.2591440.19861316100
3.2447-3.39230.26741440.17861286100
3.3923-3.5710.20081430.1648130699
3.571-3.79460.18161360.1659125598
3.7946-4.08730.22771490.16151319100
4.0873-4.4980.17061490.13861320100
4.498-5.14750.18681450.1414130599
5.1475-6.48020.18611370.1861126098
6.4802-38.1320.19521380.18128198

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