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- PDB-5n15: First Bromodomain (BD1) from Candida albicans Bdf1 in the unbound form -

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Basic information

Entry
Database: PDB / ID: 5n15
TitleFirst Bromodomain (BD1) from Candida albicans Bdf1 in the unbound form
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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
IODIDE ION / Bromodomain-containing factor 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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
C: Bromodomain-containing factor 1
D: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,15729
Polymers61,9084
Non-polymers3,24925
Water2,270126
1
A: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,85711
Polymers15,4771
Non-polymers1,38010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3308
Polymers15,4771
Non-polymers8547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9855
Polymers15,4771
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9855
Polymers15,4771
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.626, 67.568, 188.542
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-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium iodide (pH 6.5) and 26% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.37→54.9 Å / Num. obs: 27138 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.044 / Net I/σ(I): 14.5
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 5 % / Rmerge(I) obs: 0.789 / Num. unique obs: 2644 / CC1/2: 0.761 / Rpim(I) all: 0.388 / % possible all: 99.9

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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: 2OSS
Resolution: 2.37→48.894 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1368 5.05 %
Rwork0.2027 --
obs0.2049 27086 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→48.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 44 126 4363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024313
X-RAY DIFFRACTIONf_angle_d0.4545846
X-RAY DIFFRACTIONf_dihedral_angle_d13.1142722
X-RAY DIFFRACTIONf_chiral_restr0.037638
X-RAY DIFFRACTIONf_plane_restr0.004774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.45470.35341400.28792500X-RAY DIFFRACTION100
2.4547-2.5530.33121580.26762529X-RAY DIFFRACTION100
2.553-2.66920.3081470.25352518X-RAY DIFFRACTION100
2.6692-2.80990.30071370.23732543X-RAY DIFFRACTION100
2.8099-2.98590.30461210.23972550X-RAY DIFFRACTION100
2.9859-3.21640.28561130.22622568X-RAY DIFFRACTION100
3.2164-3.540.24951310.19362571X-RAY DIFFRACTION100
3.54-4.05210.21311290.17742590X-RAY DIFFRACTION100
4.0521-5.10430.19951440.16012618X-RAY DIFFRACTION100
5.1043-48.90450.21051480.19292731X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0542-0.1681-0.22150.15890.31880.4682-0.1442-0.20780.0148-0.11860.1372-0.4813-0.2581-1.1885-0.00160.3942-0.02220.05180.5057-0.00970.4509-3.80756.19372.0239
20.00180.0012-0.01520.0944-0.00650.02410.4248-0.272-0.09960.25980.1929-0.7012-0.205-0.2955-0.00061.0756-0.15450.21430.6070.01690.6672-0.0561-13.30144.4824
3-0.0160.0457-0.02230.6396-0.26012.2088-0.0317-0.235-0.2859-0.2805-0.1993-0.60390.84251.09020.10630.66880.1356-0.03980.1040.04680.30813.4234-7.7675-2.03
40.06440.07640.05930.05210.05650.04460.29470.40520.04450.5003-0.1743-0.1202-0.04550.5272-0.00020.34460.021-0.07560.3950.04040.419216.50816.2234-9.9936
50.2584-0.4507-0.19320.45230.34430.2020.01650.09010.10350.297-0.1090.13630.0176-0.21610.00020.3776-0.01880.00250.3177-0.02770.38662.927614.0978-8.0759
60.05340.06990.05090.04160.08110.17890.20670.006-0.14230.56950.02680.120.0039-0.0676-0.00020.4764-0.0333-0.01720.2960.08130.41956.2055-0.35670.9162
70.0509-0.0652-0.03890.04770.05210.03-0.4444-0.27350.3009-0.19260.13280.45750.1678-0.2173-0.00060.5833-0.08570.02770.38490.02620.42250.4236-9.3742-0.4602
80.1132-0.134-0.07870.11520.04690.0766-0.12310.2043-0.1434-0.40510.02230.09150.426-0.193900.4122-0.05090.00490.3158-0.02520.36693.01160.1199-11.8844
90.04670.0537-0.02710.0483-0.02590.0267-0.07680.15230.229-0.15380.4149-0.35840.36580.041-0.00010.43420.0369-0.06170.3228-0.05180.40826.776711.0318-20.336
100.2157-0.19850.13610.1268-0.20170.257-0.32720.42930.136-0.34130.25430.02610.47390.2028-0.01360.41840.04720.03880.2779-0.03250.366313.0974-1.2268-14.844
110.0952-0.0821-0.01770.1170.0206-0.00720.1287-0.79860.488-0.12880.104-0.0810.02030.83670.00070.88320.01060.0890.5232-0.01590.66857.89-22.3672-0.1685
120.1366-0.0121-0.26310.20960.13160.42820.0166-0.33230.0108-0.20010.1515-0.1608-0.15890.31650.00010.41480.0780.02470.3525-0.00260.390712.51018.00889.2232
130.05390.0001-0.02570.079-0.04580.1416-0.218-0.2286-0.6261-0.2692-0.1843-0.54930.3073-0.0458-0.00250.90870.26670.0930.4473-0.01340.59848.3958-6.968421.835
140.24510.23260.19560.2471-0.01951.0089-0.81060.1235-0.00740.7769-0.36461.00840.47-0.724-2.12150.5696-0.15540.2283-0.40020.36860.4268-5.58640.517920.6673
150.27650.0575-0.03930.1230.19290.3532-0.0068-0.15030.1829-0.3194-0.17410.0561-0.4869-0.4592-0.03470.38830.10650.00190.31690.04050.4427-9.869315.150115.4807
160.3289-0.0968-0.48640.20870.38880.67120.1475-0.11350.1662-0.6716-0.1844-0.30390.19080.17840.00040.41440.04650.03040.250.01750.39244.818519.94198.8527
170.08390.0585-0.02220.18120.13320.07880.0240.2163-0.002-0.6945-0.14320.15590.3646-0.2022-0.04140.5329-0.04750.02160.2148-0.01510.39571.93693.686313.7352
181.8223-0.2811-0.14070.32140.19660.1367-0.3783-0.45470.20260.1227-0.0336-0.7546-0.04340.0553-0.1580.56410.13630.00860.27990.10860.33857.5178-0.7721.9569
190.14180.09690.16720.27330.10750.0992-0.0779-0.25660.09270.2253-0.0390.06510.10180.1219-0.01470.3510.0877-0.00430.3653-0.01590.28593.826913.89321.8357
200.0223-0.03090.02330.0610.01240.0393-0.0589-0.06940.55470.17060.03840.14870.2712-0.52650.00010.3522-0.0031-0.0010.25580.00360.4218-0.229326.974618.8739
210.0742-0.00790.11870.26180.24750.37990.05940.10180.02840.4068-0.43530.3141-0.00420.0761-0.0150.3814-0.00280.10560.3634-0.0150.3494-6.435114.429824.1851
220.0217-0.0182-0.02370.01840.03090.0186-0.2670.7147-0.15660.3535-0.08960.17090.22920.3979-0.00110.93770.17740.22550.65710.1270.4887-0.8412-5.775832.3165
230.15250.13180.03540.21410.08890.0210.1056-0.30120.57110.37770.10520.15990.1273-0.0104-0.03220.4127-0.0049-0.00230.8381-0.40340.38082.5928-25.072439.9604
240.7015-0.0450.32080.19670.0770.193-0.09360.2225-0.08990.0217-0.1199-0.241-0.28260.1043-0.0692-0.2941-0.3693-0.550.7683-0.65180.515223.0006-21.03443.3853
250.5197-0.0168-0.24290.0324-0.04240.3535-0.2642-0.3350.9115-0.37620.3986-0.2824-0.61770.60550.19050.628-0.1278-0.03020.4139-0.16490.719121.2219-18.024627.6969
260.13350.0411-0.13120.03930.03650.47480.03560.1338-0.272-1.0119-0.4274-0.11270.0591-0.233-0.03830.7175-0.08-0.10050.27530.07890.62329.8702-22.18616.8902
270.53330.32630.46660.59750.52141.2357-0.228-1.03240.6876-0.1344-0.04580.12280.0068-0.5994-0.02240.40980.1002-0.10170.4954-0.18420.5424-1.5651-28.259227.864
280.02220.05010.04020.04130.02240.0636-0.0704-0.14990.4542-0.5662-0.1030.1353-0.6313-0.3990.0210.5705-0.0232-0.05660.4475-0.20440.628712.114-19.479533.2275
290.2502-0.1131-0.12680.11840.17370.3444-0.0516-0.1372-0.96530.68-0.0764-0.14720.0510.5126-0.00950.53470.0401-0.09360.7903-0.23790.59619.824-24.439539.0509
300.215-0.1953-0.11480.407-0.03180.3019-0.4069-0.26710.1708-0.15930.4727-0.2097-0.06770.20580.80590.34910.0485-0.00850.4056-0.15160.429112.2635-31.651928.3294
310.04230.03640.05350.0949-0.01540.062-0.3841-0.21260.1250.04650.3858-0.29990.5222-0.6471-0.00010.4208-0.0145-0.00660.3586-0.02330.42363.3696-35.733918.3612
320.1039-0.42250.26041.4779-0.8370.6569-0.47310.7901-0.3404-0.58020.7780.0228-0.5450.68210.44550.4268-0.10430.10170.5352-0.14430.375616.1504-28.452819.1327
330.03170.1895-0.02791.3384-0.12810.0134-0.288-0.4927-0.4186-0.53810.44820.266-0.0219-0.5074-0.02060.4355-0.03360.04771.2043-0.30390.765431.1198-24.49132.1422
340.06210.1163-0.0040.07050.12160.04890.3131-0.50870.79110.5117-0.12940.0386-0.236-0.1014-0.00050.4736-0.06110.07510.9304-0.19190.444228.246329.104646.6007
350.10210.0210.098-0.00010.01950.10860.2325-0.28070.04880.4206-0.036-0.27330.1641-0.06110.00040.60590.05460.10711.2848-0.24520.58439.135629.470551.577
360.0791-0.1429-0.03120.52620.13860.16-0.2787-0.4112-0.6796-0.0907-0.23450.5290.2302-0.7691-0.07390.4544-0.12950.1270.89630.15880.409310.407415.480143.5636
370.0275-0.03560.01860.0369-0.02720.0125-0.46150.253-0.4153-0.09570.58320.1180.6676-0.143600.6377-0.06090.11620.540.050.531521.42289.957833.2162
380.65750.0662-0.47190.2520.22181.0291-0.0499-1.26850.36530.18510.0852-0.0534-0.24110.63930.08780.25790.1405-0.00440.54150.03270.287533.220722.087935.5956
390.446-0.0601-0.28090.0439-0.06460.60890.2084-0.34870.1643-0.0654-0.209-0.1833-0.09450.4093-0.04280.33390.01330.02090.94420.06550.242519.554620.580445.8125
403.0943-0.1028-1.12280.0947-0.25221.44820.3142-0.04370.21640.11220.28650.06470.01860.18730.65290.37880.14020.12341.3178-0.19660.400712.059228.330846.0629
410.19330.14850.08630.2619-0.1220.15620.2174-0.22780.0952-0.3860.1306-0.2041-0.3419-0.28430.01190.34740.0244-0.00560.49360.03880.344819.196124.735133.2982
420.0422-0.0031-0.0120.0604-0.05030.0497-0.3021-0.12360.3254-0.16660.49360.1996-0.3256-0.4783-0.00020.32780.06010.10090.32740.04220.378927.807719.569223.477
430.0080.0513-0.04220.3341-0.31610.2459-0.36470.12280.43390.0899-0.1407-0.13650.3849-0.7127-0.02460.4453-0.11520.02140.5666-0.05840.395815.01215.514430.029
440.05170.00040.0445-0.011-0.00630.0605-0.45290.0046-0.0597-0.11440.0514-0.06920.1267-0.24090.00060.397-0.07250.0221.22410.0190.91870.127523.488942.7824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 168 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 211 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 233 )
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 244 )
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 250 )
8X-RAY DIFFRACTION8chain 'A' and (resid 251 through 266 )
9X-RAY DIFFRACTION9chain 'A' and (resid 267 through 272 )
10X-RAY DIFFRACTION10chain 'A' and (resid 273 through 289 )
11X-RAY DIFFRACTION11chain 'A' and (resid 290 through 304 )
12X-RAY DIFFRACTION12chain 'B' and (resid 168 through 182 )
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 189 )
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 204 )
15X-RAY DIFFRACTION15chain 'B' and (resid 205 through 211 )
16X-RAY DIFFRACTION16chain 'B' and (resid 212 through 233 )
17X-RAY DIFFRACTION17chain 'B' and (resid 234 through 244 )
18X-RAY DIFFRACTION18chain 'B' and (resid 245 through 250 )
19X-RAY DIFFRACTION19chain 'B' and (resid 251 through 266 )
20X-RAY DIFFRACTION20chain 'B' and (resid 267 through 272 )
21X-RAY DIFFRACTION21chain 'B' and (resid 273 through 289 )
22X-RAY DIFFRACTION22chain 'B' and (resid 290 through 299 )
23X-RAY DIFFRACTION23chain 'C' and (resid 167 through 182 )
24X-RAY DIFFRACTION24chain 'C' and (resid 183 through 189 )
25X-RAY DIFFRACTION25chain 'C' and (resid 190 through 204 )
26X-RAY DIFFRACTION26chain 'C' and (resid 205 through 211 )
27X-RAY DIFFRACTION27chain 'C' and (resid 212 through 233 )
28X-RAY DIFFRACTION28chain 'C' and (resid 234 through 244 )
29X-RAY DIFFRACTION29chain 'C' and (resid 245 through 250 )
30X-RAY DIFFRACTION30chain 'C' and (resid 251 through 266 )
31X-RAY DIFFRACTION31chain 'C' and (resid 267 through 272 )
32X-RAY DIFFRACTION32chain 'C' and (resid 273 through 289 )
33X-RAY DIFFRACTION33chain 'C' and (resid 290 through 296 )
34X-RAY DIFFRACTION34chain 'D' and (resid 168 through 182 )
35X-RAY DIFFRACTION35chain 'D' and (resid 183 through 189 )
36X-RAY DIFFRACTION36chain 'D' and (resid 190 through 204 )
37X-RAY DIFFRACTION37chain 'D' and (resid 205 through 211 )
38X-RAY DIFFRACTION38chain 'D' and (resid 212 through 233 )
39X-RAY DIFFRACTION39chain 'D' and (resid 234 through 244 )
40X-RAY DIFFRACTION40chain 'D' and (resid 245 through 250 )
41X-RAY DIFFRACTION41chain 'D' and (resid 251 through 266 )
42X-RAY DIFFRACTION42chain 'D' and (resid 267 through 272 )
43X-RAY DIFFRACTION43chain 'D' and (resid 273 through 289 )
44X-RAY DIFFRACTION44chain 'D' and (resid 290 through 297 )

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