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

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Basic information

Entry
Database: PDB / ID: 6kco
TitleShuguo PWWP in complex with ssDNA
Components
  • DNA (5'-D(*TP*CP*CP*CP*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: 2.4 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
D: LD23804p
E: LD23804p
F: LD23804p
G: LD23804p
H: LD23804p
I: LD23804p
J: LD23804p
K: LD23804p
L: LD23804p
M: LD23804p
N: LD23804p
O: LD23804p
P: LD23804p
1O: DNA (5'-D(*TP*CP*CP*CP*T)-3')
2M: DNA (5'-D(*TP*CP*CP*CP*T)-3')
1P: DNA (5'-D(*TP*CP*CP*CP*T)-3')
1H: DNA (5'-D(*TP*CP*CP*CP*T)-3')
4D: DNA (5'-D(*TP*CP*CP*CP*T)-3')
7E: DNA (5'-D(*TP*CP*CP*CP*T)-3')
6F: DNA (5'-D(*TP*CP*CP*CP*T)-3')
2G: DNA (5'-D(*TP*CP*CP*CP*T)-3')
5I: DNA (5'-D(*TP*CP*CP*CP*T)-3')
4J: DNA (5'-D(*TP*CP*CP*CP*T)-3')
3L: DNA (5'-D(*TP*CP*CP*CP*T)-3')
9N: DNA (5'-D(*TP*CP*CP*CP*T)-3')
6A: DNA (5'-D(*TP*CP*CP*CP*T)-3')
3B: DNA (5'-D(*TP*CP*CP*CP*T)-3')
7C: DNA (5'-D(*TP*CP*CP*CP*T)-3')
8K: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)177,42432
Polymers177,42432
Non-polymers00
Water8,629479
1
A: LD23804p
B: LD23804p
6A: DNA (5'-D(*TP*CP*CP*CP*T)-3')
3B: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LD23804p
D: LD23804p
4D: DNA (5'-D(*TP*CP*CP*CP*T)-3')
7C: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LD23804p
F: LD23804p
7E: DNA (5'-D(*TP*CP*CP*CP*T)-3')
6F: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: LD23804p
H: LD23804p
1H: DNA (5'-D(*TP*CP*CP*CP*T)-3')
2G: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: LD23804p
J: LD23804p
5I: DNA (5'-D(*TP*CP*CP*CP*T)-3')
4J: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: LD23804p
L: LD23804p
3L: DNA (5'-D(*TP*CP*CP*CP*T)-3')
8K: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: LD23804p
N: LD23804p
2M: DNA (5'-D(*TP*CP*CP*CP*T)-3')
9N: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: LD23804p
P: LD23804p
1O: DNA (5'-D(*TP*CP*CP*CP*T)-3')
1P: DNA (5'-D(*TP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.666, 76.326, 85.256
Angle α, β, γ (deg.)101.753, 106.077, 113.754
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
LD23804p


Mass: 9658.010 Da / Num. of mol.: 16 / 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(*TP*CP*CP*CP*T)-3')


Mass: 1430.974 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl, pH 8.5and 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 PILATUS 6M / Detector: PIXEL / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 55088 / % possible obs: 96.26 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.234 / Num. unique obs: 5126

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KD6

6kd6


Resolution: 2.4→29.94 Å / SU ML: 0.2702 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.2361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 2009 3.65 %
Rwork0.1982 52993 -
obs0.1997 55002 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10471 811 0 479 11761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003611591
X-RAY DIFFRACTIONf_angle_d0.570715724
X-RAY DIFFRACTIONf_chiral_restr0.03851696
X-RAY DIFFRACTIONf_plane_restr0.00321835
X-RAY DIFFRACTIONf_dihedral_angle_d8.84526865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.27381140.21823161X-RAY DIFFRACTION79.43
2.46-2.530.30321480.2373650X-RAY DIFFRACTION93.41
2.53-2.60.30861290.23383779X-RAY DIFFRACTION95.55
2.6-2.690.32541570.2413802X-RAY DIFFRACTION97.3
2.69-2.780.30131340.23883848X-RAY DIFFRACTION97.81
2.78-2.890.30631580.21693811X-RAY DIFFRACTION97.88
2.89-3.020.27281470.22023871X-RAY DIFFRACTION98.24
3.02-3.180.27651370.22133902X-RAY DIFFRACTION97.87
3.18-3.380.25131480.20653855X-RAY DIFFRACTION98.69
3.38-3.640.22631510.19393862X-RAY DIFFRACTION98.41
3.64-4.010.22181440.17813876X-RAY DIFFRACTION98.46
4.01-4.590.18311490.1553876X-RAY DIFFRACTION99.21
4.59-5.770.16481480.16433866X-RAY DIFFRACTION98.21
5.77-29.940.19721450.20283834X-RAY DIFFRACTION97.41

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