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- PDB-6kd6: Shuguo PWWP domain -

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Basic information

Entry
Database: PDB / ID: 6kd6
TitleShuguo PWWP domain
ComponentsLD23804p
KeywordsDNA BINDING PROTEIN / PWWP / histone reader / DNA binding / NUCLEAR PROTEIN
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
JIL-1 anchoring and stabilizing protein, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 domain
Authors: Liu, Y.C. / Huang, Y.
History
DepositionJul 1, 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


Theoretical massNumber of molelcules
Total (without water)38,6324
Polymers38,6324
Non-polymers00
Water9,116506
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 area3010 Å2
ΔGint-22 kcal/mol
Surface area9120 Å2
MethodPISA
2
C: LD23804p
D: LD23804p


Theoretical massNumber of molelcules
Total (without water)19,3162
Polymers19,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-21 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.869, 51.126, 58.726
Angle α, β, γ (deg.)90.00, 93.50, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Bicine, pH 8.5, 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 40338 / % possible obs: 99.3 % / Redundancy: 6.3 % / Net I/σ(I): 35.4
Reflection shellResolution: 1.58→1.64 Å / Num. unique obs: 4004

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KCU

6kcu


Resolution: 1.58→39.139 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.2145 2025 5.02 %
Rwork0.1766 --
obs0.1785 40307 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.58→39.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 0 506 3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062682
X-RAY DIFFRACTIONf_angle_d0.7583601
X-RAY DIFFRACTIONf_dihedral_angle_d3.051619
X-RAY DIFFRACTIONf_chiral_restr0.049379
X-RAY DIFFRACTIONf_plane_restr0.005448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5799-1.61940.24271450.1972739X-RAY DIFFRACTION100
1.6194-1.66320.24031490.19552738X-RAY DIFFRACTION100
1.6632-1.71220.23561400.18932706X-RAY DIFFRACTION100
1.7122-1.76740.22261560.1842701X-RAY DIFFRACTION99
1.7674-1.83060.22161320.18152736X-RAY DIFFRACTION99
1.8306-1.90390.21611500.17882727X-RAY DIFFRACTION100
1.9039-1.99050.23481510.17972717X-RAY DIFFRACTION99
1.9905-2.09550.23551420.17372748X-RAY DIFFRACTION99
2.0955-2.22680.19031400.17042719X-RAY DIFFRACTION99
2.2268-2.39870.22761510.17932720X-RAY DIFFRACTION100
2.3987-2.640.25011350.18412761X-RAY DIFFRACTION99
2.64-3.02190.2141470.1912718X-RAY DIFFRACTION99
3.0219-3.80680.211420.16592763X-RAY DIFFRACTION99
3.8068-39.15140.18481450.16632789X-RAY DIFFRACTION98

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