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- PDB-5n16: First Bromodomain (BD1) from Candida albicans Bdf1 bound to a dib... -

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Basic information

Entry
Database: PDB / ID: 5n16
TitleFirst Bromodomain (BD1) from Candida albicans Bdf1 bound to a dibenzothiazepinone (compound 1)
ComponentsBromodomain-containing factor 1
KeywordsTRANSCRIPTION / Bromodomain
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / 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 / Bromodomain profile. ...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-8FN / NICKEL (II) ION / Bromodomain-containing factor 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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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
C: Bromodomain-containing factor 1
D: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94714
Polymers61,9084
Non-polymers2,03910
Water11,674648
1
A: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4215
Polymers15,4771
Non-polymers9444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5362
Polymers15,4771
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0414
Polymers15,4771
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9493
Polymers15,4771
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.435, 77.292, 102.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Bromodomain-containing factor 1


Mass: 15476.932 Da / Num. of mol.: 4
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-8FN / 5-cyclopropyl-2-(5-pyrazin-2-yl-1,2,4-oxadiazol-3-yl)benzo[b][1,4]benzothiazepin-6-one


Mass: 413.452 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H15N5O2S
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were obtained by mixing a solution of 20 mg/mL protein and 0.4 mM inhibitor with 0.1 M TRIS-HCl (pH 8.5), 23% (w/v) PEG MME 2000 and 10 mM NiCl2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.76→54.1 Å / Num. obs: 59921 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.037 / Net I/σ(I): 12.1
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5873 / CC1/2: 0.759 / Rpim(I) all: 0.324 / % possible all: 99.3

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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: 5N15

5n15


Resolution: 1.76→42.74 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.51
RfactorNum. reflection% reflection
Rfree0.2148 3040 5.08 %
Rwork0.1785 --
obs0.1804 59849 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 131 648 4889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064356
X-RAY DIFFRACTIONf_angle_d0.9795920
X-RAY DIFFRACTIONf_dihedral_angle_d13.2132709
X-RAY DIFFRACTIONf_chiral_restr0.045632
X-RAY DIFFRACTIONf_plane_restr0.006781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.78750.36041390.29852524X-RAY DIFFRACTION99
1.7875-1.81680.2821170.25862535X-RAY DIFFRACTION99
1.8168-1.84820.30181490.21852544X-RAY DIFFRACTION100
1.8482-1.88180.24511550.20852546X-RAY DIFFRACTION100
1.8818-1.9180.26591100.18892572X-RAY DIFFRACTION100
1.918-1.95710.24171400.19562572X-RAY DIFFRACTION100
1.9571-1.99970.23941510.19452542X-RAY DIFFRACTION99
1.9997-2.04620.22491200.19162592X-RAY DIFFRACTION100
2.0462-2.09740.21771220.18632580X-RAY DIFFRACTION100
2.0974-2.15410.2221530.17472556X-RAY DIFFRACTION100
2.1541-2.21740.23921440.17512546X-RAY DIFFRACTION100
2.2174-2.2890.25341470.17962554X-RAY DIFFRACTION100
2.289-2.37080.20871340.17892563X-RAY DIFFRACTION100
2.3708-2.46570.21561320.18372593X-RAY DIFFRACTION100
2.4657-2.57790.22271120.17742609X-RAY DIFFRACTION100
2.5779-2.71380.19681410.17312575X-RAY DIFFRACTION99
2.7138-2.88380.22091610.17572559X-RAY DIFFRACTION100
2.8838-3.10640.20811390.18252619X-RAY DIFFRACTION100
3.1064-3.41890.21561370.16752600X-RAY DIFFRACTION100
3.4189-3.91330.19821530.16132608X-RAY DIFFRACTION99
3.9133-4.92920.17851370.15462670X-RAY DIFFRACTION100
4.9292-42.75290.19211470.18342750X-RAY DIFFRACTION99

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