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- PDB-9i7d: Crystal structure of wild-type HRP-2 PWWP domain - Crystal form P... -

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Basic information

Entry
Database: PDB / ID: 9i7d
TitleCrystal structure of wild-type HRP-2 PWWP domain - Crystal form P212121 type 2
ComponentsHepatoma-derived growth factor-related protein 2
KeywordsGENE REGULATION / Epigenetics
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
Hepatoma-derived growth factor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsOsipov, E.M. / 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: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal engineering of the hepatoma-derived growth factor-related protein 2 PWWP domain towards crystallographic fragment screening.
Authors: Vantieghem, T. / Osipov, E.M. / Beelen, S. / Strelkov, S.V.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,28511
Polymers21,4282
Non-polymers8579
Water1,18966
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1916
Polymers10,7141
Non-polymers4765
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)11,0955
Polymers10,7141
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.883, 59.833, 105.778
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.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M Ammonium sulfate 0.2 M Ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97893 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.36→52.89 Å / Num. obs: 10576 / % possible obs: 93 % / Redundancy: 4.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Χ2: 0.85 / Net I/σ(I): 15.7 / Num. measured all: 43845
Reflection shellResolution: 2.36→2.49 Å / % possible obs: 93.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.33 / Num. measured all: 6021 / Num. unique obs: 1525 / CC1/2: 0.66 / Rpim(I) all: 0.193 / Rrim(I) all: 0.387 / Χ2: 0.62 / Net I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→52.89 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.977 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28074 531 5.1 %RANDOM
Rwork0.21732 ---
obs0.22084 9894 90.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.67 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å2-0 Å20 Å2
2--6.63 Å2-0 Å2
3----2.62 Å2
Refinement stepCycle: 1 / Resolution: 2.36→52.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 47 66 1498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121483
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161279
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.8372015
X-RAY DIFFRACTIONr_angle_other_deg0.5441.782974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6845168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.90154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58710202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3235.565684
X-RAY DIFFRACTIONr_mcbond_other5.3085.564684
X-RAY DIFFRACTIONr_mcangle_it8.0419.942848
X-RAY DIFFRACTIONr_mcangle_other8.0449.947849
X-RAY DIFFRACTIONr_scbond_it6.3816.126799
X-RAY DIFFRACTIONr_scbond_other5.5735.965772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.46610.7241126
X-RAY DIFFRACTIONr_long_range_B_refined12.48358.851609
X-RAY DIFFRACTIONr_long_range_B_other12.42358.91603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 34 -
Rwork0.331 698 -
obs--88.41 %

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