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- PDB-9hh8: Crystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in c... -

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Basic information

Entry
Database: PDB / ID: 9hh8
TitleCrystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in complex with RMM23
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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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: 1.61 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

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Assembly

Deposited unit
A: Bromo domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6875
Polymers15,1631
Non-polymers5244
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-22 kcal/mol
Surface area7100 Å2
Unit cell
Length a, b, c (Å)92.883, 92.883, 70.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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: isolated from a natural source / Formula: C18H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 3350, 0.4 M LiSO4, Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 1.61→46.44 Å / Num. obs: 23916 / % possible obs: 99.9 % / Redundancy: 39.1 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.01 / Rrim(I) all: 0.064 / Χ2: 0.99 / Net I/σ(I): 34.4
Reflection shellResolution: 1.61→1.63 Å / % possible obs: 98.3 % / Redundancy: 37.1 % / Rmerge(I) obs: 3.092 / Num. measured all: 41678 / Num. unique obs: 1122 / CC1/2: 0.854 / Rpim(I) all: 0.506 / Rrim(I) all: 3.135 / Χ2: 0.96 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→46.44 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1177 4.93 %
Rwork0.1928 --
obs0.194 23856 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 33 134 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151030
X-RAY DIFFRACTIONf_angle_d1.1421404
X-RAY DIFFRACTIONf_dihedral_angle_d13.936380
X-RAY DIFFRACTIONf_chiral_restr0.068150
X-RAY DIFFRACTIONf_plane_restr0.008196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.680.33221510.31592735X-RAY DIFFRACTION99
1.68-1.770.35641380.2762789X-RAY DIFFRACTION100
1.77-1.880.34221460.28662784X-RAY DIFFRACTION100
1.88-2.020.28951470.23932793X-RAY DIFFRACTION100
2.02-2.230.22861500.20952800X-RAY DIFFRACTION100
2.23-2.550.26881430.20752842X-RAY DIFFRACTION100
2.55-3.210.22621510.19962877X-RAY DIFFRACTION100
3.21-46.440.1591510.15823059X-RAY DIFFRACTION100

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