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- PDB-9hh7: Crystal Structure of the Plasmodium falciparum Bromodomain PfBDP1... -

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Basic information

Entry
Database: PDB / ID: 9hh7
TitleCrystal Structure of the Plasmodium falciparum Bromodomain PfBDP1 in complex with RMM23
ComponentsBromodomain protein 1
KeywordsTRANSCRIPTION / plasmodium / bromodomain / inhibitor / complex
Function / homology
Function and homology information


histone H3K9ac reader activity / histone H3K14ac reader activity / nucleus
Similarity search - Function
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 / bromo domain ...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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 21, 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: Bromodomain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1242
Polymers15,8271
Non-polymers2961
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7890 Å2
Unit cell
Length a, b, c (Å)38.120, 88.215, 108.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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Components

#1: Protein Bromodomain protein 1


Mass: 15827.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1033700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IJ72
#2: Chemical ChemComp-A1IUW / 3-methyl-4-(3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-1-yl)benzamide


Mass: 296.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG MMW (PEG 2K, 3350, 4K and 5K MME ;each 12.5 %) ,7% (v/v) Tacsimate, 0.1 M HEPES pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.787→35.965 Å / Num. obs: 9402 / % possible obs: 91.8 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Net I/σ(I): 13.4
Reflection shellResolution: 1.787→1.944 Å / Num. unique obs: 1146 / CC1/2: 0.612

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
STARANISOdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→35.96 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.3742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2432 433 4.61 %
Rwork0.2089 8965 -
obs0.2105 9398 52.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.69 Å2
Refinement stepCycle: LAST / Resolution: 1.79→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 22 77 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211126
X-RAY DIFFRACTIONf_angle_d0.39311532
X-RAY DIFFRACTIONf_chiral_restr0.0349161
X-RAY DIFFRACTIONf_plane_restr0.0027228
X-RAY DIFFRACTIONf_dihedral_angle_d10.6619431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-2.050.3511540.32231012X-RAY DIFFRACTION18.28
2.05-2.580.32691250.28792720X-RAY DIFFRACTION48.34
2.58-35.960.22792540.19395233X-RAY DIFFRACTION90.17
Refinement TLS params.Method: refined / Origin x: 2.91732545288 Å / Origin y: 20.2820248253 Å / Origin z: 12.9398573696 Å
111213212223313233
T0.173029760141 Å2-0.00584985093169 Å20.0120563201081 Å2-0.312778001262 Å20.132557350907 Å2--0.168889446937 Å2
L2.90853896846 °2-0.925958997223 °2-0.831656171181 °2-1.25322727904 °20.433193206721 °2--3.62847400076 °2
S-0.201694964041 Å °0.776563681564 Å °-0.270454456667 Å °-0.219134379056 Å °-0.0503090031418 Å °-0.204306772263 Å °0.138169211908 Å °0.152632548196 Å °0.18176569888 Å °
Refinement TLS groupSelection details: all

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