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- PDB-8r6l: Crystal structure of Candida glabrata Bdf1 bromodomain 2 in the u... -

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Basic information

Entry
Database: PDB / ID: 8r6l
TitleCrystal structure of Candida glabrata Bdf1 bromodomain 2 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 / Bromodomain profile. / bromo domain ...NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
ACETATE ION / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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
C: Candida glabrata strain CBS138 chromosome C complete sequence
D: Candida glabrata strain CBS138 chromosome C complete sequence
E: Candida glabrata strain CBS138 chromosome C complete sequence
F: Candida glabrata strain CBS138 chromosome C complete sequence
G: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,06336
Polymers96,4157
Non-polymers2,64829
Water3,225179
1
A: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,58910
Polymers13,7741
Non-polymers8159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4048
Polymers13,7741
Non-polymers6317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1355
Polymers13,7741
Non-polymers3614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1024
Polymers13,7741
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2276
Polymers13,7741
Non-polymers4535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8332
Polymers13,7741
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Candida glabrata strain CBS138 chromosome C complete sequence


Theoretical massNumber of molelcules
Total (without water)13,7741
Polymers13,7741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.291, 67.686, 96.618
Angle α, β, γ (deg.)90.000, 95.520, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 13773.615 Da / Num. of mol.: 7
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 33% MPD, 100 mM sodium acetate

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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: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.96→44.37 Å / Num. obs: 73550 / % possible obs: 99 % / Redundancy: 3 % / Biso Wilson estimate: 42.58 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 1.96→2.12 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 15349 / CC1/2: 0.823 / Rrim(I) all: 0.795 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→44.37 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 28.6534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 3610 4.92 %
Rwork0.2001 69796 -
obs0.2015 73406 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.22 Å2
Refinement stepCycle: LAST / Resolution: 1.96→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 176 179 6973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046946
X-RAY DIFFRACTIONf_angle_d0.93099379
X-RAY DIFFRACTIONf_chiral_restr0.054954
X-RAY DIFFRACTIONf_plane_restr0.00631213
X-RAY DIFFRACTIONf_dihedral_angle_d12.20442575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.44441350.4472661X-RAY DIFFRACTION98.69
1.99-2.010.42011380.40422665X-RAY DIFFRACTION99.29
2.01-2.040.36191550.36952646X-RAY DIFFRACTION99.29
2.04-2.070.36811370.34532628X-RAY DIFFRACTION97.09
2.07-2.10.36571350.31342730X-RAY DIFFRACTION99.31
2.1-2.140.33231500.30162653X-RAY DIFFRACTION99.61
2.14-2.180.29041400.27962706X-RAY DIFFRACTION99.51
2.18-2.220.31371500.27062636X-RAY DIFFRACTION99.29
2.22-2.260.32361280.2812651X-RAY DIFFRACTION97.68
2.26-2.30.30551280.26892708X-RAY DIFFRACTION99.47
2.3-2.350.30431270.25412711X-RAY DIFFRACTION99.27
2.35-2.410.28651610.23382666X-RAY DIFFRACTION99.12
2.41-2.470.26971470.21732635X-RAY DIFFRACTION99.43
2.47-2.540.22921110.20582747X-RAY DIFFRACTION99.79
2.54-2.610.22731370.19112715X-RAY DIFFRACTION99.69
2.61-2.690.22671510.18472699X-RAY DIFFRACTION99.2
2.7-2.790.22091540.1992655X-RAY DIFFRACTION99.68
2.79-2.90.2631270.21512714X-RAY DIFFRACTION99.58
2.9-3.040.22711360.20152696X-RAY DIFFRACTION99.44
3.04-3.20.23961390.20162723X-RAY DIFFRACTION99
3.2-3.40.22141260.19972679X-RAY DIFFRACTION98.56
3.4-3.660.22451380.19742659X-RAY DIFFRACTION97.56
3.66-4.030.20231420.16642687X-RAY DIFFRACTION98.09
4.03-4.610.19491470.15642694X-RAY DIFFRACTION98.61
4.61-5.80.19131330.18252704X-RAY DIFFRACTION98
5.8-44.370.1791380.16462728X-RAY DIFFRACTION96.27

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