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- PDB-5n18: Second Bromodomain (BD2) from Candida albicans Bdf1 bound to an i... -

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Basic information

Entry
Database: PDB / ID: 5n18
TitleSecond Bromodomain (BD2) from Candida albicans Bdf1 bound to an imidazopyridine (compound 2)
ComponentsBromodomain-containing factor 1
KeywordsTRANSCRIPTION / Bromodomain
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / : / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8HZ / Bromodomain-containing factor 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. ...Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. / Cornet, M. / McKenna, C.E. / Govin, J. / Petosa, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE16-0027-01 France
CitationJournal: Nat Commun / Year: 2017
Title: Selective BET bromodomain inhibition as an antifungal therapeutic strategy.
Authors: Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. ...Authors: Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. / Cornet, M. / McKenna, C.E. / Govin, J. / Petosa, C.
History
DepositionFeb 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Data collection
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing factor 1
B: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6744
Polymers25,2532
Non-polymers4212
Water4,918273
1
A: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9562
Polymers12,6261
Non-polymers3291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7182
Polymers12,6261
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.484, 35.997, 64.495
Angle α, β, γ (deg.)90.00, 107.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain-containing factor 1


Mass: 12626.337 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: BDF1, CaO19.8593, CaO19.978 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5A4W8
#2: Chemical ChemComp-8HZ / 4-[8-methyl-3-[(4-methylphenyl)amino]imidazo[1,2-a]pyridin-2-yl]phenol


Mass: 329.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N3O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Crystals were obtained by mixing a solution of 22 mg/mL protein and 1.5 mM inhibitor with 0.1 M sodium acetate (pH 4.6) and 25% (w/v) PEG 3000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.45→44.307 Å / Num. obs: 34661 / % possible obs: 95.2 % / Redundancy: 2.45 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.035 / Net I/σ(I): 12.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.442 / Num. unique obs: 3549 / CC1/2: 0.805 / Rpim(I) all: 0.321 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N13

5n13


Resolution: 1.45→44.307 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.1978 1790 5.17 %
Rwork0.1593 --
obs0.1613 34641 95.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→44.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 31 273 2040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021809
X-RAY DIFFRACTIONf_angle_d0.7392445
X-RAY DIFFRACTIONf_dihedral_angle_d13.249673
X-RAY DIFFRACTIONf_chiral_restr0.068252
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48920.30281430.23062558X-RAY DIFFRACTION97
1.4892-1.5330.26531460.2082539X-RAY DIFFRACTION97
1.533-1.58250.22441260.17872584X-RAY DIFFRACTION97
1.5825-1.63910.24831490.16342562X-RAY DIFFRACTION97
1.6391-1.70470.20041330.15152486X-RAY DIFFRACTION95
1.7047-1.78230.1951200.14652512X-RAY DIFFRACTION94
1.7823-1.87630.21381430.14852572X-RAY DIFFRACTION98
1.8763-1.99380.19521390.15142556X-RAY DIFFRACTION97
1.9938-2.14780.20151360.14682511X-RAY DIFFRACTION95
2.1478-2.36390.21340.14952521X-RAY DIFFRACTION94
2.3639-2.70590.21471440.16342468X-RAY DIFFRACTION93
2.7059-3.4090.19311540.16072460X-RAY DIFFRACTION92
3.409-44.3070.15381230.15712522X-RAY DIFFRACTION91

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