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- PDB-9grv: Crystal structure of HRP-2 PWWP domain in complex with compound 37 -

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Basic information

Entry
Database: PDB / ID: 9grv
TitleCrystal structure of HRP-2 PWWP domain in complex with compound 37
ComponentsHepatoma-derived growth factor-related protein 2
KeywordsGENE REGULATION / Inhibitor
Function / homology
Function and homology information


histone H3K27me3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / histone H3K9me2/3 reader activity / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / positive regulation of double-strand break repair via homologous recombination / positive regulation of cell growth / DNA recombination ...histone H3K27me3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / histone H3K9me2/3 reader activity / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / positive regulation of double-strand break repair via homologous recombination / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / cytoplasm
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
5-bromanylpyrimidine / Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOsipov, E.M. / Paulovcakova, T. / Beelen, S. / Vantieghem, T. / Strelkov, S.V.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1SC9822N Belgium
Research Foundation - Flanders (FWO)1SC9824N Belgium
Research Foundation - Flanders (FWO)G053822N Belgium
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Rational fragment-based design of compounds targeting the PWWP domain of the HRP family.
Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / ...Authors: Vantieghem, T. / Aslam, N.A. / Osipov, E.M. / Akele, M. / Van Belle, S. / Beelen, S. / Drexler, M. / Paulovcakova, T. / Lux, V. / Fearon, D. / Douangamath, A. / von Delft, F. / Christ, F. / Veverka, V. / Verwilst, P. / Van Aerschot, A. / Debyser, Z. / Strelkov, S.V.
History
DepositionSep 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatoma-derived growth factor-related protein 2
B: Hepatoma-derived growth factor-related protein 2
C: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,84210
Polymers32,1433
Non-polymers7007
Water3,531196
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1615
Polymers10,7141
Non-polymers4474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8883
Polymers10,7141
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7922
Polymers10,7141
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.651, 41.928, 157.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatoma-derived growth factor-related protein 2 / HDGF-related protein 2 / HRP-2 / Hepatoma-derived growth factor 2 / HDGF-2


Mass: 10714.236 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z4V5
#2: Chemical ChemComp-HHN / 5-bromanylpyrimidine


Mass: 158.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3BrN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.2 M ammonium sulfate, 0.2 M ammonium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91165 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 1.55→78.83 Å / Num. obs: 40936 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Χ2: 0.67 / Net I/σ(I): 14.6 / Num. measured all: 550814
Reflection shellResolution: 1.55→1.64 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 1.884 / Num. measured all: 80779 / Num. unique obs: 5839 / CC1/2: 0.679 / Rpim(I) all: 0.519 / Rrim(I) all: 1.955 / Χ2: 0.34 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→40.52 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 1962 4.8 %
Rwork0.2214 --
obs0.223 40853 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 35 196 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042344
X-RAY DIFFRACTIONf_angle_d0.6633179
X-RAY DIFFRACTIONf_dihedral_angle_d13.111860
X-RAY DIFFRACTIONf_chiral_restr0.05287
X-RAY DIFFRACTIONf_plane_restr0.006419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3331170.31192702X-RAY DIFFRACTION100
1.59-1.630.36261160.28072758X-RAY DIFFRACTION100
1.63-1.680.31081420.2712748X-RAY DIFFRACTION100
1.68-1.740.26421330.25832753X-RAY DIFFRACTION100
1.74-1.80.36751500.2832713X-RAY DIFFRACTION100
1.8-1.870.35441420.27712730X-RAY DIFFRACTION100
1.87-1.960.32581000.25692782X-RAY DIFFRACTION100
1.96-2.060.29641750.24132742X-RAY DIFFRACTION100
2.06-2.190.29691380.23672782X-RAY DIFFRACTION100
2.19-2.360.25151530.23562741X-RAY DIFFRACTION100
2.36-2.590.29061440.23292813X-RAY DIFFRACTION100
2.59-2.970.27481330.23432815X-RAY DIFFRACTION100
2.97-3.740.22751470.20882844X-RAY DIFFRACTION100
3.74-40.520.21671720.19522968X-RAY DIFFRACTION100

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