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- PDB-8r6i: Crystal structure of Candida glabrata Bdf1 bromodomain 1 in the u... -

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Basic information

Entry
Database: PDB / ID: 8r6i
TitleCrystal structure of Candida glabrata Bdf1 bromodomain 1 in the unbound state
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: 1.08 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
B: Candida glabrata strain CBS138 chromosome C complete sequence


Theoretical massNumber of molelcules
Total (without water)25,8982
Polymers25,8982
Non-polymers00
Water7,026390
1
A: Candida glabrata strain CBS138 chromosome C complete sequence


Theoretical massNumber of molelcules
Total (without water)12,9491
Polymers12,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Candida glabrata strain CBS138 chromosome C complete sequence


Theoretical massNumber of molelcules
Total (without water)12,9491
Polymers12,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.890, 40.593, 48.872
Angle α, β, γ (deg.)98.140, 94.370, 94.770
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 12949.065 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 1.73 Å3/Da / Density % sol: 28.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 1500 and 0.1 MIB (malonic acid:imidazole:boric acid in 2:3:3 molar ratio) buffer (pH 9).

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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: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.08→48.2 Å / Num. obs: 66240 / % possible obs: 88.5 % / Redundancy: 1.7 % / Biso Wilson estimate: 9.91 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.851 / Net I/σ(I): 9.1
Reflection shellResolution: 1.08→1.11 Å / Num. unique obs: 4162 / CC1/2: 0.54 / Rrim(I) all: 0.851 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→48.19 Å / SU ML: 0.1205 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.0504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1945 2099 3.17 %
Rwork0.1736 64141 -
obs0.1743 66240 88.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.69 Å2
Refinement stepCycle: LAST / Resolution: 1.08→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 390 2200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881848
X-RAY DIFFRACTIONf_angle_d1.05072497
X-RAY DIFFRACTIONf_chiral_restr0.0816274
X-RAY DIFFRACTIONf_plane_restr0.0098333
X-RAY DIFFRACTIONf_dihedral_angle_d14.7424723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.10.29761160.31173555X-RAY DIFFRACTION73.17
1.1-1.130.33181380.2834211X-RAY DIFFRACTION86.93
1.13-1.160.30141370.26834195X-RAY DIFFRACTION87.06
1.16-1.190.25371370.25624195X-RAY DIFFRACTION86.48
1.19-1.230.2531380.2314199X-RAY DIFFRACTION87.72
1.23-1.280.27221430.21694355X-RAY DIFFRACTION89.51
1.28-1.330.2181410.2064332X-RAY DIFFRACTION90
1.33-1.390.25051420.19194330X-RAY DIFFRACTION89.89
1.39-1.460.20181420.18574351X-RAY DIFFRACTION89.63
1.46-1.550.2041420.17234341X-RAY DIFFRACTION89.91
1.55-1.670.19251430.15764387X-RAY DIFFRACTION90.84
1.67-1.840.21021460.16374457X-RAY DIFFRACTION92.36
1.84-2.110.16311440.15754401X-RAY DIFFRACTION90.83
2.11-2.660.18961430.15434363X-RAY DIFFRACTION90.7
2.66-48.190.14681470.1454469X-RAY DIFFRACTION92.51

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