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- PDB-7m97: Crystal structure of the bromodomain from Plasmodium falciparum b... -

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Basic information

Entry
Database: PDB / ID: 7m97
TitleCrystal structure of the bromodomain from Plasmodium falciparum bromodomain protein 1
ComponentsBromodomain protein 1
KeywordsNUCLEAR PROTEIN / bromodomain
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 (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGlass, K.C.
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural insights into acetylated histone ligand recognition by the BDP1 bromodomain of Plasmodium falciparum.
Authors: Singh, A.K. / Phillips, M. / Alkrimi, S. / Tonelli, M. / Boyson, S.P. / Malone, K.L. / Nix, J.C. / Glass, K.C.
History
DepositionMar 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain protein 1


Theoretical massNumber of molelcules
Total (without water)15,0371
Polymers15,0371
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.051, 88.667, 106.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Bromodomain protein 1


Mass: 15037.358 Da / Num. of mol.: 1 / Mutation: E458S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1033700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IJ72
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3 M lithium sulfate, 0.1 M tris, pH 8.5, 38% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→35.84 Å / Num. obs: 12597 / % possible obs: 99.63 % / Redundancy: 2 % / Biso Wilson estimate: 29.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02602 / Rpim(I) all: 0.02602 / Rrim(I) all: 0.0368 / Net I/σ(I): 19.24
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.2672 / Mean I/σ(I) obs: 2.93 / Num. unique obs: 1203 / CC1/2: 0.93 / CC star: 0.982 / Rpim(I) all: 0.2672 / Rrim(I) all: 0.3779

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ulc

5ulc


Resolution: 2→35.84 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 587 4.67 %
Rwork0.1939 11985 -
obs0.1958 12572 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.01 Å2
Refinement stepCycle: LAST / Resolution: 2→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 0 110 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821028
X-RAY DIFFRACTIONf_angle_d0.88871394
X-RAY DIFFRACTIONf_chiral_restr0.0541157
X-RAY DIFFRACTIONf_plane_restr0.0041176
X-RAY DIFFRACTIONf_dihedral_angle_d20.7945376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.3181330.2432920X-RAY DIFFRACTION99.28
2.2-2.520.26511480.21042957X-RAY DIFFRACTION99.68
2.52-3.170.25931600.20912983X-RAY DIFFRACTION99.84
3.17-35.840.20051460.17443125X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: 34.9863714822 Å / Origin y: 20.3868843445 Å / Origin z: 40.5860127109 Å
111213212223313233
T0.242462216703 Å2-0.0655946013603 Å2-0.0112370416886 Å2-0.333845434068 Å2-0.053901291414 Å2--0.190910611826 Å2
L4.36223099906 °20.0932506034714 °2-1.26479463126 °2-1.69229054164 °2-0.367191602125 °2--5.09682396203 °2
S-0.18926786495 Å °-0.0265362721096 Å °-0.190646777513 Å °0.0785546889532 Å °0.0515133776823 Å °0.118537635067 Å °0.168825667346 Å °-0.193925195263 Å °0.134981410337 Å °
Refinement TLS groupSelection details: all

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