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- PDB-8r6n: Crystal structure of Candida glabrata Bdf1 bromodomain 2 bound to... -

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Basic information

Entry
Database: PDB / ID: 8r6n
TitleCrystal structure of Candida glabrata Bdf1 bromodomain 2 bound to a pyridoindole ligand
ComponentsCandida glabrata strain CBS138 chromosome C complete sequence
KeywordsTRANSCRIPTION / Bromodomain
Function / homology
Function and homology information


: / chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain ...NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPetosa, C. / Wei, K. / McKenna, C.E. / Govin, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Adv Sci / Year: 2025
Title: Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential.
Authors: Wei, K. / Arlotto, M. / Overhulse, J.M. / Dinh, T.A. / Zhou, Y. / Dupper, N.J. / Yang, J. / Kashemirov, B.A. / Dawi, H. / Garnaud, C. / Bourgine, G. / Mietton, F. / Champleboux, M. / Larabi, ...Authors: Wei, K. / Arlotto, M. / Overhulse, J.M. / Dinh, T.A. / Zhou, Y. / Dupper, N.J. / Yang, J. / Kashemirov, B.A. / Dawi, H. / Garnaud, C. / Bourgine, G. / Mietton, F. / Champleboux, M. / Larabi, A. / Hayat, Y. / Indorato, R.L. / Noirclerc-Savoye, M. / Skoufias, D. / Cornet, M. / Rabut, G. / McKenna, C.E. / Petosa, C. / Govin, J.
History
DepositionNov 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1922
Polymers13,7741
Non-polymers4181
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.582, 67.582, 152.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

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Components

#1: Protein Candida glabrata strain CBS138 chromosome C complete sequence


Mass: 13773.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nakaseomyces glabratus (fungus) / Gene: CAGL0C02541g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FWV7
#2: Chemical ChemComp-Y7B / 2-ethanoyl-~{N}-(4-morpholin-4-ylphenyl)-1,3,4,5-tetrahydropyrido[4,3-b]indole-8-carboxamide


Mass: 418.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.8 M sodium dihydrogen phosphate, 0.8 M potassium dihydrogen phosphate, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.11→61.81 Å / Num. obs: 5781 / % possible obs: 54.69 % / Redundancy: 12.3 % / Biso Wilson estimate: 25.33 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.277 / Net I/σ(I): 8.3
Reflection shellResolution: 2.11→2.42 Å / Num. unique obs: 289 / CC1/2: 0.696 / Rrim(I) all: 1.266 / % possible all: 8.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→61.81 Å / SU ML: 0.3293 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.0733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Diffraction was highly anisotropic. The diffraction limits are 2.80 Angstrom in the a* and b* directions and 2.11 Angstrom in the c* direction.
RfactorNum. reflection% reflection
Rfree0.287 295 5.1 %
Rwork0.2574 5486 -
obs0.2593 5781 54.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.94 Å2
Refinement stepCycle: LAST / Resolution: 2.11→61.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 31 23 1004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311011
X-RAY DIFFRACTIONf_angle_d0.67741372
X-RAY DIFFRACTIONf_chiral_restr0.0427136
X-RAY DIFFRACTIONf_plane_restr0.0052177
X-RAY DIFFRACTIONf_dihedral_angle_d14.6107375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.191.507710.457443X-RAY DIFFRACTION4
2.19-2.270.1540.420976X-RAY DIFFRACTION8
2.28-2.380.490260.3305126X-RAY DIFFRACTION13
2.38-2.50.235980.3198192X-RAY DIFFRACTION19
2.51-2.660.3098180.3331303X-RAY DIFFRACTION32
2.66-2.870.3491400.3175608X-RAY DIFFRACTION62
2.87-3.150.4119520.3227996X-RAY DIFFRACTION100
3.16-3.610.2706540.27111014X-RAY DIFFRACTION100
3.61-4.550.2565540.21461031X-RAY DIFFRACTION100
4.55-61.810.2449580.21941097X-RAY DIFFRACTION100

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