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- PDB-7xxe: Crystal structure of spFft3 C-terminal truncation -

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Basic information

Entry
Database: PDB / ID: 7xxe
TitleCrystal structure of spFft3 C-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 / MOLECULAR REPLACEMENT / Resolution: 4.202 Å
AuthorsNan, Z. / Tao, J. / Yangao, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800632 China
CitationJournal: To Be Published
Title: Crystal structure of spFft3 C-terminal truncation
Authors: Nan, Z. / Tao, J. / Yangao, H.
History
DepositionMay 30, 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

Downloads & links

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Assembly

Deposited unit
B: ATP-dependent helicase fft3
A: ATP-dependent helicase fft3


Theoretical massNumber of molelcules
Total (without water)64,7582
Polymers64,7582
Non-polymers00
Water0
1
B: ATP-dependent helicase fft3


Theoretical massNumber of molelcules
Total (without water)32,3791
Polymers32,3791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-dependent helicase fft3


Theoretical massNumber of molelcules
Total (without water)32,3791
Polymers32,3791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.649, 99.649, 130.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 627 through 656 or resid 660 through 903))
21(chain B and (resid 627 or (resid 628 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resid 627 through 656 or resid 660 through 903))AB627 - 6562 - 31
12VALVALALAALA(chain A and (resid 627 through 656 or resid 660 through 903))AB660 - 90335 - 278
21THRTHRTHRTHR(chain B and (resid 627 or (resid 628 and (name...BA6272
22ARGARGARGARG(chain B and (resid 627 or (resid 628 and (name...BA6283
23LYSLYSALAALA(chain B and (resid 627 or (resid 628 and (name...BA626 - 9031 - 278
24LYSLYSALAALA(chain B and (resid 627 or (resid 628 and (name...BA626 - 9031 - 278
25LYSLYSALAALA(chain B and (resid 627 or (resid 628 and (name...BA626 - 9031 - 278
26LYSLYSALAALA(chain B and (resid 627 or (resid 628 and (name...BA626 - 9031 - 278

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Components

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


Mass: 32379.246 Da / Num. of mol.: 2
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

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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: 2.84 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 4.202→46.55 Å / Num. obs: 5377 / % possible obs: 95.48 % / Redundancy: 20.3 % / CC1/2: 0.976 / Net I/σ(I): 34.1
Reflection shellResolution: 4.202→4.27 Å / Num. unique obs: 250 / CC1/2: 0.99

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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: MOLECULAR REPLACEMENT
Starting model: 5GN1

5gn1


Resolution: 4.202→46.55 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3369 518 10 %
Rwork0.308 4661 -
obs0.3108 5179 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.3 Å2 / Biso mean: 68.2918 Å2 / Biso min: 2 Å2
Refinement stepCycle: final / Resolution: 4.202→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 0 0 4409
Num. residues----541
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2041X-RAY DIFFRACTION25.019TORSIONAL
12B2041X-RAY DIFFRACTION25.019TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.202-4.62450.25591130.2689109590
4.6245-5.29290.31471310.3172116696
5.2929-6.66540.41291380.3773118598
6.6654-46.550.36541360.2899121599

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