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- PDB-9i7f: Crystal structure of HRP-2 PWWP domain with C64S mutation - Cryst... -

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Basic information

Entry
Database: PDB / ID: 9i7f
TitleCrystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21 type 1
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: 2.08 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
F: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3759
Polymers64,1896
Non-polymers1863
Water3,279182
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8223
Polymers10,6981
Non-polymers1242
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


Theoretical massNumber of molelcules
Total (without water)10,6981
Polymers10,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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
5
E: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7602
Polymers10,6981
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 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)41.686, 80.923, 108.723
Angle α, β, γ (deg.)90.00, 102.34, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 6 / Mutation: C64S
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M Ammonium acetate 27% PEG 4000 0.1 M Sodium 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: 0.98011 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: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.08→53.11 Å / Num. obs: 42492 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.07 / Rrim(I) all: 0.186 / Χ2: 0.9 / Net I/σ(I): 7.4
Reflection shellResolution: 2.08→2.19 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.753 / Num. measured all: 43701 / Num. unique obs: 6197 / CC1/2: 0.639 / Rpim(I) all: 0.708 / Rrim(I) all: 1.893 / Χ2: 0.69 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→53.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.345 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25431 2132 5 %RANDOM
Rwork0.19858 ---
obs0.2013 40160 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.779 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.28 Å2
2--1.88 Å20 Å2
3----1.89 Å2
Refinement stepCycle: 1 / Resolution: 2.08→53.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 12 182 4465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124462
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163970
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.8426054
X-RAY DIFFRACTIONr_angle_other_deg0.621.7789225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.365520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.575512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85210630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021060
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_it3.7493.4882110
X-RAY DIFFRACTIONr_mcbond_other3.7443.4882110
X-RAY DIFFRACTIONr_mcangle_it5.5766.2292620
X-RAY DIFFRACTIONr_mcangle_other5.5766.232621
X-RAY DIFFRACTIONr_scbond_it4.3223.8162352
X-RAY DIFFRACTIONr_scbond_other4.3223.8162352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6096.7923435
X-RAY DIFFRACTIONr_long_range_B_refined8.57137.74867
X-RAY DIFFRACTIONr_long_range_B_other8.56237.724857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 137 -
Rwork0.359 2890 -
obs--98.09 %

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