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- PDB-9i7h: Crystal structure of HRP-2 PWWP domain with C64S mutation - Cryst... -

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Basic information

Entry
Database: PDB / ID: 9i7h
TitleCrystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P21 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: 1.54 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

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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)21,6334
Polymers21,3962
Non-polymers2362
Water1,49583
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8162
Polymers10,6981
Non-polymers1181
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)10,8162
Polymers10,6981
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.109, 70.989, 44.458
Angle α, β, γ (deg.)90.00, 118.26, 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.: 2 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 55.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium dihydrogen phosphate 50% MPD 0.1 M TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.54→37.09 Å / Num. obs: 30555 / % possible obs: 90.6 % / Redundancy: 2.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.093 / Rrim(I) all: 0.164 / Χ2: 0.74 / Net I/σ(I): 3.3 / Num. measured all: 79562
Reflection shellResolution: 1.54→1.63 Å / % possible obs: 85.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 1.108 / Num. measured all: 9300 / Num. unique obs: 4208 / CC1/2: 0.582 / Rpim(I) all: 0.87 / Rrim(I) all: 1.417 / Χ2: 0.7 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→37.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 0.761 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1487 4.9 %RANDOM
Rwork0.18764 ---
obs0.18953 29005 89.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.752 Å2
Baniso -1Baniso -2Baniso -3
1--9.39 Å2-0 Å2-0.92 Å2
2--18.49 Å20 Å2
3----9.1 Å2
Refinement stepCycle: 1 / Resolution: 1.54→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 16 83 1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161368
X-RAY DIFFRACTIONr_angle_refined_deg2.2881.8392087
X-RAY DIFFRACTIONr_angle_other_deg0.8511.7793176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.185182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.4154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90710214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
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_it2.5421.869722
X-RAY DIFFRACTIONr_mcbond_other2.5421.869722
X-RAY DIFFRACTIONr_mcangle_it3.3733.374900
X-RAY DIFFRACTIONr_mcangle_other3.3713.376901
X-RAY DIFFRACTIONr_scbond_it2.8942.091810
X-RAY DIFFRACTIONr_scbond_other2.8932.092811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9433.7251186
X-RAY DIFFRACTIONr_long_range_B_refined4.94919.631665
X-RAY DIFFRACTIONr_long_range_B_other4.94219.421656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.542→1.582 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 72 -
Rwork0.284 1875 -
obs--77.08 %

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