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- PDB-6kcp: Shuguo PWWP in complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 6kcp
TitleShuguo PWWP in complex with ssDNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*T)-3')
  • LD23804p
KeywordsDNA BINDING PROTEIN/DNA / Shuguo / PWWP / histone reader / DNA binding / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / chromatin remodeling / nucleus
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
DNA / JIL-1 anchoring and stabilizing protein, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y.C. / Huang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870741 China
National Natural Science Foundation of China91640102 China
CitationJournal: To Be Published
Title: Shuguo PWWP in complex with ssDNA
Authors: Liu, Y.C. / Huang, Y.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LD23804p
B: LD23804p
C: LD23804p
E: DNA (5'-D(P*TP*TP*TP*TP*T)-3')
D: LD23804p


Theoretical massNumber of molelcules
Total (without water)40,1085
Polymers40,1085
Non-polymers00
Water8,521473
1
A: LD23804p
B: LD23804p


Theoretical massNumber of molelcules
Total (without water)19,3162
Polymers19,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-23 kcal/mol
Surface area9340 Å2
MethodPISA
2
C: LD23804p
D: LD23804p

E: DNA (5'-D(P*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,7923
Polymers20,7923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3260 Å2
ΔGint-27 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.829, 51.076, 59.205
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
LD23804p


Mass: 9658.010 Da / Num. of mol.: 4 / Fragment: PWWP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG7946, CG7946, Dmel_CG7946 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VAA9
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*T)-3')


Mass: 1476.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl, pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 27752 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.291 / Num. unique obs: 2779

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KD6

6kd6


Resolution: 1.8→26.162 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2187 2014 7.27 %
Rwork0.1818 --
obs0.1845 27711 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 40 0 473 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062794
X-RAY DIFFRACTIONf_angle_d0.8273765
X-RAY DIFFRACTIONf_dihedral_angle_d5.2771681
X-RAY DIFFRACTIONf_chiral_restr0.051394
X-RAY DIFFRACTIONf_plane_restr0.006471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7981-1.84310.27511440.20761787X-RAY DIFFRACTION98
1.8431-1.89290.23541380.19421831X-RAY DIFFRACTION100
1.8929-1.94860.22011410.19271803X-RAY DIFFRACTION100
1.9486-2.01140.24651440.21839X-RAY DIFFRACTION100
2.0114-2.08330.23311460.17991833X-RAY DIFFRACTION100
2.0833-2.16670.23321380.17181846X-RAY DIFFRACTION100
2.1667-2.26520.17511400.17811836X-RAY DIFFRACTION100
2.2652-2.38460.25011410.18811832X-RAY DIFFRACTION100
2.3846-2.53390.2461450.19211823X-RAY DIFFRACTION100
2.5339-2.72930.23661470.19381826X-RAY DIFFRACTION100
2.7293-3.00360.22661480.18981854X-RAY DIFFRACTION100
3.0036-3.43740.25131410.17281837X-RAY DIFFRACTION100
3.4374-4.32760.16581460.16321863X-RAY DIFFRACTION100
4.3276-26.16460.2041550.18231887X-RAY DIFFRACTION99

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