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- PDB-5n17: First Bromodomain (BD1) from Candida albicans Bdf1 bound to a dib... -

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Basic information

Entry
Database: PDB / ID: 5n17
TitleFirst Bromodomain (BD1) from Candida albicans Bdf1 bound to a dibenzothiazepinone (compound 3)
ComponentsBromodomain-containing factor 1
KeywordsTRANSCRIPTION / Bromodomain
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / chromatin organization / regulation of gene expression / histone binding / DNA repair / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8FK / Bromodomain-containing factor 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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. / Chauvon, M. / d'Enfer, 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 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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)31,9756
Polymers31,0742
Non-polymers9014
Water4,666259
1
A: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0844
Polymers15,5371
Non-polymers5473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8912
Polymers15,5371
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.413, 70.413, 124.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-580-

HOH

21B-610-

HOH

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Components

#1: Protein Bromodomain-containing factor 1


Mass: 15537.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: BDF1, CaO19.8593, CaO19.978 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5A4W8
#2: Chemical ChemComp-8FK / (2~{S})-~{N}-(5-methyl-6-oxidanylidene-benzo[b][1,4]benzothiazepin-2-yl)oxolane-2-carboxamide


Mass: 354.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18N2O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Crystals were obtained by mixing a solution of 25 mg/mL protein and 1.5 mM inhibitor with 0.1 M sodium acetate (pH 4.6) and 2.4 M ammonium sulfate.

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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: 1.6→49.8 Å / Num. obs: 41446 / % possible obs: 98.3 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.025 / Net I/σ(I): 16.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.689 / Num. unique obs: 4131 / CC1/2: 0.812 / Rpim(I) all: 0.285 / % possible all: 99.6

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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: 5N15

5n15


Resolution: 1.6→49.79 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.66 / Phase error: 21.43
RfactorNum. reflection% reflection
Rfree0.2352 2090 5.05 %
Rwork0.2131 --
obs0.2142 41399 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 60 259 2381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042176
X-RAY DIFFRACTIONf_angle_d0.8572955
X-RAY DIFFRACTIONf_dihedral_angle_d11.7461365
X-RAY DIFFRACTIONf_chiral_restr0.043316
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63720.2621570.25492577X-RAY DIFFRACTION99
1.6372-1.67820.23661490.24042584X-RAY DIFFRACTION100
1.6782-1.72350.25551460.23972586X-RAY DIFFRACTION100
1.7235-1.77430.27781590.23352575X-RAY DIFFRACTION100
1.7743-1.83150.27031360.22192590X-RAY DIFFRACTION99
1.8315-1.8970.34541360.30282579X-RAY DIFFRACTION98
1.897-1.9730.46211190.37132386X-RAY DIFFRACTION91
1.973-2.06270.23621240.22812654X-RAY DIFFRACTION100
2.0627-2.17150.19851460.20692616X-RAY DIFFRACTION100
2.1715-2.30760.31081350.27492531X-RAY DIFFRACTION96
2.3076-2.48570.21741360.20672660X-RAY DIFFRACTION100
2.4857-2.73580.23321190.20452690X-RAY DIFFRACTION100
2.7358-3.13170.21941560.20222692X-RAY DIFFRACTION100
3.1317-3.94530.20741470.18282681X-RAY DIFFRACTION98
3.9453-49.81360.20031250.18172908X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.64334.25246.8094.29892.04335.20320.153-1.07080.2959-0.2627-0.53990.87650.0642-1.11460.39950.26430.0434-0.09760.3938-0.11350.5924-2.1438-12.0659-31.7849
23.89830.72891.83382.56791.582.8311-0.34580.09250.7917-0.5633-0.151.5816-0.6136-0.78250.46860.4886-0.0035-0.26840.7477-0.15370.9587-17.8787-23.5958-44.0908
37.3185-0.81920.65924.59360.70583.1906-0.4182-0.04990.8891-0.6415-0.23751.1628-0.3559-1.07270.45330.29410.0296-0.2070.5375-0.22940.7502-14.9607-20.7036-41.5298
45.00652.4263.08892.81891.43024.5454-0.1490.4468-0.4256-0.56080.05690.41780.1351-0.17210.03280.2622-0.0311-0.05780.2913-0.13870.3239-3.3427-29.6545-43.5032
52.0524-8.81923.22792.0771-5.2216.5917-0.3585-0.30210.87070.46490.0299-0.7294-0.54340.7050.1850.2837-0.0659-0.08540.40040.03210.49323.5873-11.5495-19.5962
62.515-0.2198-1.16492.7875-2.06075.88470.23310.48940.2162-0.20580.18840.1861-0.409-0.7279-0.45020.2170.01090.01850.23740.08910.3042-16.5326-0.4306-24.6498
76.0006-2.0477-0.20185.2685-1.59473.72260.0518-0.47220.42410.3833-0.08-0.5604-0.37930.6703-0.00470.1673-0.0588-0.03920.2494-0.00750.158-4.8889-9.1843-6.9391
87.5138-5.3448-1.04852.0472-0.54464.5723-0.07330.39420.0368-0.3683-0.1766-0.17480.18360.66760.20310.16330.00810.02850.31250.03810.1465-3.1191-15.6774-15.9894
95.33270.09610.6316.4033-2.1149.6171-0.07470.630.268-0.5160.21050.0313-0.4841-0.0384-0.07360.1879-0.01790.02490.24170.0780.1476-12.1303-2.4617-23.6716
102.9944-1.29751.35112.9887-2.07085.05650.0220.32090.0541-0.12560.14940.31540.0015-0.4018-0.17520.0901-0.03120.00190.20720.02350.1536-18.0171-12.5576-14.712
116.87227.68032.08058.70161.92373.7642-0.29230.28370.6552-0.4894-0.07630.7396-0.1553-0.41440.30590.15780.0265-0.06950.2029-0.07990.31741.6222-17.2287-36.0454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 167 through 177 )
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 204 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 249 )
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 295 )
5X-RAY DIFFRACTION5chain 'B' and (resid 167 through 177 )
6X-RAY DIFFRACTION6chain 'B' and (resid 178 through 204 )
7X-RAY DIFFRACTION7chain 'B' and (resid 205 through 224 )
8X-RAY DIFFRACTION8chain 'B' and (resid 225 through 234 )
9X-RAY DIFFRACTION9chain 'B' and (resid 235 through 249 )
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 296 )
11X-RAY DIFFRACTION11chain 'A' and (resid 225 through 234 )

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