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- PDB-9hgf: Crystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in c... -

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Basic information

Entry
Database: PDB / ID: 9hgf
TitleCrystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in complex with RMM25
ComponentsBromo domain-containing protein
KeywordsTRANSCRIPTION / plasmodium / bromodomain / inhibitor / complex
Function / homology
Function and homology information


Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromo domain-containing protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAmann, M. / Huegle, M. / Einsle, O. / Guenther, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG2202 Germany
CitationJournal: Chemmedchem / Year: 2025
Title: A Novel Inhibitor against the Bromodomain Protein 1 of the Malaria Pathogen Plasmodium Falciparum.
Authors: Amann, M. / Warstat, R. / Rechten, K.K. / Theuer, P. / Schustereder, M. / Clavey, S. / Breit, B. / Einsle, O. / Hugle, M. / Petter, M. / Gunther, S.
History
DepositionNov 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 11, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromo domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6054
Polymers15,1631
Non-polymers4423
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.798, 92.798, 70.721
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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Components

#1: Protein Bromo domain-containing protein


Mass: 15163.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_111040 / Production host: Escherichia coli (E. coli) / References: UniProt: A5KDW3
#2: Chemical ChemComp-A1IUH / 3,5-dimethyl-4-(3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-1-yl)benzamide


Mass: 310.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 3350, 0.2M LiSO4, Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.859→80.365 Å / Num. obs: 15625 / % possible obs: 99.9 % / Redundancy: 37.3 % / Biso Wilson estimate: 28.27 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.022 / Rrim(I) all: 0.136 / Net I/σ(I): 20.6
Reflection shellResolution: 1.859→1.891 Å / Redundancy: 39.6 % / Rmerge(I) obs: 2.255 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 762 / Rpim(I) all: 0.361 / Rrim(I) all: 2.284

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
PHASERphasing
autoPROCdata reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→53.09 Å / SU ML: 0.2189 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.2695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 795 5.1 %
Rwork0.2044 14788 -
obs0.2059 15583 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.19 Å2
Refinement stepCycle: LAST / Resolution: 1.86→53.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 29 86 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01261019
X-RAY DIFFRACTIONf_angle_d1.06651388
X-RAY DIFFRACTIONf_chiral_restr0.0579151
X-RAY DIFFRACTIONf_plane_restr0.0064176
X-RAY DIFFRACTIONf_dihedral_angle_d17.2198364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.970.3261020.33612426X-RAY DIFFRACTION99.61
1.98-2.130.32791490.27532384X-RAY DIFFRACTION99.57
2.13-2.340.28191280.2272428X-RAY DIFFRACTION99.61
2.34-2.680.24881350.20762438X-RAY DIFFRACTION99.81
2.68-3.380.25051450.21562466X-RAY DIFFRACTION99.5
3.38-53.090.18351360.16782646X-RAY DIFFRACTION99.82

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