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- PDB-8r6k: Crystal structure of Candida glabrata Bdf1 bromodomain 1 bound to... -

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Basic information

Entry
Database: PDB / ID: 8r6k
TitleCrystal structure of Candida glabrata Bdf1 bromodomain 1 bound to a phenyltriazine 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
: / PHOSPHATE ION / : / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,09812
Polymers51,7964
Non-polymers1,3028
Water7,782432
1
A: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4725
Polymers12,9491
Non-polymers5234
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)13,2432
Polymers12,9491
Non-polymers2941
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)13,3383
Polymers12,9491
Non-polymers3892
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)13,0442
Polymers12,9491
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.700, 128.700, 148.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#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-509-

HOH

21A-514-

HOH

31A-515-

HOH

41B-1049-

HOH

51B-1084-

HOH

61B-1091-

HOH

71C-516-

HOH

81C-524-

HOH

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Components

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


Mass: 12949.065 Da / Num. of mol.: 4
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-Y78 / 6-methyl-~{N}-[(5-methylfuran-2-yl)methyl]-3-(4-methylphenyl)-1,2,4-triazin-5-amine


Mass: 294.351 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H18N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.072 M NaH2PO4, 1.73 M K2HPO4 (pH 8.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.19→64.4 Å / Num. obs: 32208 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.05 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.22 / Net I/σ(I): 7.3
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2779 / CC1/2: 0.415 / Rrim(I) all: 0.747 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→57.46 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.5213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 1661 5.16 %
Rwork0.209 30538 -
obs0.211 32199 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.42 Å2
Refinement stepCycle: LAST / Resolution: 2.19→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 87 432 4102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723747
X-RAY DIFFRACTIONf_angle_d0.8125066
X-RAY DIFFRACTIONf_chiral_restr0.0489543
X-RAY DIFFRACTIONf_plane_restr0.0085666
X-RAY DIFFRACTIONf_dihedral_angle_d7.5882483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.260.35211320.30682530X-RAY DIFFRACTION99.92
2.26-2.330.31911510.29772471X-RAY DIFFRACTION100
2.33-2.410.30221360.26762512X-RAY DIFFRACTION100
2.41-2.510.27731160.25882523X-RAY DIFFRACTION100
2.51-2.620.29081200.24392538X-RAY DIFFRACTION99.96
2.62-2.760.30281380.23742524X-RAY DIFFRACTION99.92
2.76-2.930.26171490.23542525X-RAY DIFFRACTION100
2.93-3.160.26891400.22552515X-RAY DIFFRACTION99.96
3.16-3.480.23221440.18492538X-RAY DIFFRACTION99.93
3.48-3.980.21671300.16742564X-RAY DIFFRACTION99.96
3.98-5.020.17371560.14852584X-RAY DIFFRACTION100
5.02-57.460.22561490.17792714X-RAY DIFFRACTION99.65

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