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- PDB-7hh3: PanDDA analysis group deposition -- Crystal structure of HRP-2 PW... -

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Basic information

Entry
Database: PDB / ID: 7hh3
TitlePanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z1245580425
ComponentsHepatoma-derived growth factor-related protein 2
KeywordsGENE REGULATION / Inhibitor / Fragment screening / Epigenetic reader / methyllysine / PWWP / Diamond Light Source / I04-1 / PanDDA / XChem
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: 1.64 Å
AuthorsVantieghem, T. / Osipov, E. / Fearon, D. / Douangamath, A. / von Delft, F. / Strelkov, S.
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
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
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)32,93712
Polymers32,0953
Non-polymers8439
Water4,918273
1
A: Hepatoma-derived growth factor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0485
Polymers10,6981
Non-polymers3504
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)11,0334
Polymers10,6981
Non-polymers3343
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)10,8563
Polymers10,6981
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.860, 42.150, 159.590
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: 10698.171 Da / Num. of mol.: 3 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1A3X / 2-[(2S)-2-methylpiperidin-1-yl]ethan-1-amine


Mass: 142.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 28% PEG MME 2000; 0.15 M ammonium sulfate; 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.918076 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918076 Å / Relative weight: 1
ReflectionResolution: 1.64→53.2 Å / Num. obs: 35301 / % possible obs: 99.1 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Χ2: 0.97 / Net I/σ(I): 9.6 / Num. measured all: 186966
Reflection shellResolution: 1.64→1.68 Å / % possible obs: 92.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.309 / Num. measured all: 10567 / Num. unique obs: 2418 / CC1/2: 0.309 / Rpim(I) all: 0.694 / Rrim(I) all: 1.488 / Χ2: 0.61 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→40.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.404 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25542 1851 5.3 %RANDOM
Rwork0.20792 ---
obs0.21043 33381 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0 Å2
2---0.4 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.64→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 48 273 2461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.8363100
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9995264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.48656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29910306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021858
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.413.511068
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.6756.2741329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4183.8371213
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.53450.983486
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 133 -
Rwork0.346 2274 -
obs--92.19 %

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