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

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Basic information

Entry
Database: PDB / ID: 9hhb
TitleCrystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in complex with RMM21
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: 2.26 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)15,6063
Polymers15,1631
Non-polymers4432
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area7030 Å2
Unit cell
Length a, b, c (Å)92.382, 92.382, 69.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-350-

HOH

31A-355-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1IUY / ~{N}-[2-methyl-3-(3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-1-yl)phenyl]methanesulfonamide


Mass: 346.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 35% PEG3350, 0.4 M LiSO4, Tris pH 8,2

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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 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 2.26→46.19 Å / Num. obs: 8689 / % possible obs: 100 % / Redundancy: 38.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.023 / Rrim(I) all: 0.139 / Χ2: 1 / Net I/σ(I): 20 / Num. measured all: 333586
Reflection shellResolution: 2.26→2.33 Å / % possible obs: 100 % / Redundancy: 40.8 % / Rmerge(I) obs: 0.965 / Num. measured all: 31733 / Num. unique obs: 778 / CC1/2: 0.975 / Rpim(I) all: 0.153 / Rrim(I) all: 0.977 / Χ2: 1.02 / Net I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→46.19 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 428 4.95 %
Rwork0.2163 --
obs0.2187 8653 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 29 55 1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021044
X-RAY DIFFRACTIONf_angle_d0.3761427
X-RAY DIFFRACTIONf_dihedral_angle_d19.235371
X-RAY DIFFRACTIONf_chiral_restr0.034150
X-RAY DIFFRACTIONf_plane_restr0.001179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.590.33951380.29442661X-RAY DIFFRACTION100
2.59-3.260.28951600.2662672X-RAY DIFFRACTION100
3.26-46.190.23681300.18142892X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.5415 Å / Origin y: -22.8954 Å / Origin z: -0.8998 Å
111213212223313233
T0.3414 Å20.0014 Å20.0181 Å2-0.2695 Å20.0032 Å2--0.6341 Å2
L2.4685 °21.2431 °21.0309 °2-2.0131 °21.2405 °2--4.0438 °2
S0.0924 Å °-0.083 Å °0.1185 Å °0.1775 Å °-0.0217 Å °0.0519 Å °-0.0414 Å °0.0164 Å °-0.0642 Å °
Refinement TLS groupSelection details: all

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