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- PDB-9i7j: Crystal structure of HRP-2 PWWP domain with C64S mutation - Cryst... -

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Basic information

Entry
Database: PDB / ID: 9i7j
TitleCrystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21212
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: 1.8 Å
AuthorsVantieghem, T. / Osipov, E.M. / 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

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
D: Hepatoma-derived growth factor-related protein 2
E: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6477
Polymers53,4915
Non-polymers1562
Water5,296294
1
A: Hepatoma-derived growth factor-related protein 2


Theoretical massNumber of molelcules
Total (without water)10,6981
Polymers10,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatoma-derived growth factor-related protein 2


Theoretical massNumber of molelcules
Total (without water)10,6981
Polymers10,6981
Non-polymers00
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)10,7762
Polymers10,6981
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7762
Polymers10,6981
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hepatoma-derived growth factor-related protein 2


Theoretical massNumber of molelcules
Total (without water)10,6981
Polymers10,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.332, 193.363, 41.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 10698.171 Da / Num. of mol.: 5
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-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 32.5% PEG 4000 0.1 MSodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.99988 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.8→96.68 Å / Num. obs: 52808 / % possible obs: 94.5 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.045 / Rrim(I) all: 0.111 / Χ2: 0.87 / Net I/σ(I): 11.1 / Num. measured all: 316035
Reflection shellResolution: 1.8→1.9 Å / % possible obs: 93.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.071 / Num. measured all: 44563 / Num. unique obs: 7520 / CC1/2: 0.653 / Rpim(I) all: 0.467 / Rrim(I) all: 1.173 / Χ2: 0.66 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→96.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.799 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22842 2534 4.8 %RANDOM
Rwork0.19732 ---
obs0.19882 50173 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.64 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.8→96.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 8 294 3826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163263
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.844999
X-RAY DIFFRACTIONr_angle_other_deg0.5691.7757580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7295431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.957510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73810510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02876
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_it2.9412.9361745
X-RAY DIFFRACTIONr_mcbond_other2.9412.9361745
X-RAY DIFFRACTIONr_mcangle_it4.095.2522169
X-RAY DIFFRACTIONr_mcangle_other4.095.2542170
X-RAY DIFFRACTIONr_scbond_it3.4923.271936
X-RAY DIFFRACTIONr_scbond_other3.493.271936
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4185.8212831
X-RAY DIFFRACTIONr_long_range_B_refined7.23935.524083
X-RAY DIFFRACTIONr_long_range_B_other7.18834.574009
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å
RfactorNum. reflection% reflection
Rfree0.287 176 -
Rwork0.271 3905 -
obs--99.68 %

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