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- PDB-8r6j: Crystal structure of Candida glabrata Bdf1 bromodomain 1 bound to... -

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Basic information

Entry
Database: PDB / ID: 8r6j
TitleCrystal structure of Candida glabrata Bdf1 bromodomain 1 bound to a pyrazole 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
: / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8336
Polymers25,8982
Non-polymers9354
Water2,900161
1
A: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4173
Polymers12,9491
Non-polymers4682
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)13,4173
Polymers12,9491
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.841, 142.619, 93.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

21A-486-

HOH

31B-958-

HOH

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Components

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


Mass: 12949.065 Da / Num. of mol.: 2
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-Y7F / 2-methyl-~{N}-[[5-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)thiophen-2-yl]methyl]pyrazole-3-carboxamide


Mass: 371.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13N5O2S2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 161 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 10000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.82→39.11 Å / Num. obs: 20025 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 22.95 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.116 / Net I/σ(I): 10.4
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1160 / CC1/2: 0.532 / Rrim(I) all: 0.99 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→39.11 Å / SU ML: 0.215 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 1001 5.01 %
Rwork0.1988 18989 -
obs0.2006 19990 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.48 Å2
Refinement stepCycle: LAST / Resolution: 1.82→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 60 161 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331882
X-RAY DIFFRACTIONf_angle_d0.60562548
X-RAY DIFFRACTIONf_chiral_restr0.0399270
X-RAY DIFFRACTIONf_plane_restr0.004338
X-RAY DIFFRACTIONf_dihedral_angle_d13.7586722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.920.3141390.29662630X-RAY DIFFRACTION97.71
1.92-2.040.28041420.2612692X-RAY DIFFRACTION99.65
2.04-2.190.27711420.21792699X-RAY DIFFRACTION98.92
2.19-2.410.24951410.21332674X-RAY DIFFRACTION98.36
2.41-2.760.22851410.19942687X-RAY DIFFRACTION97.92
2.76-3.480.23261450.18712746X-RAY DIFFRACTION99.35
3.48-39.110.20171510.17182861X-RAY DIFFRACTION98.46
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)
19.953882606842.00108406412-5.429744388082.008388967524.914709881717.02519902992-1.01187798386-0.697726014228-1.147656818510.5785636521310.5165455875990.4939877754331.72721613512-0.02687100136340.6779026200240.5333185489410.04339590344240.06882273080290.2454671795470.08989390576860.3903770184649.6176624564316.20409735821.6883757955
23.23312255411-2.778707940471.724111514748.68096930713-7.662033532753.11774488321-0.146728343935-0.1312753846810.1686713498170.4958941871-0.523876635781-1.205172559410.1856596914250.5652795100450.6703348087820.402531144460.103949447297-0.04845125154020.310334728048-0.0381796865330.32718677630514.293194344724.289065671613.9323108983
32.91898254301-3.04080656035-8.887263202965.210522266824.819361666612.50651061899-0.0432461638339-0.00838760196639-0.301627058216-0.204923340347-0.1338147670330.292300490571-0.3001427881020.2763701275090.119069658340.138298103852-0.000655458884122-0.02082499690140.235749066235-0.007997615916580.209404665448.2744218928539.217661822210.0948333493
45.2730291213-1.112874291291.008160299666.14152433417-1.288071999198.655881822220.09556348029240.6185593409360.577761761742-0.110004530851-0.13334262037-0.236156405213-0.1932509699150.09840350908560.1216297051080.1285740902050.006654931000860.02332393427590.1616127942480.0264820363090.17051392852-2.7669744876948.468886345918.4617111605
54.69534340987-5.38293000086-1.968886540392.817071117221.914579033395.71985926813-0.3169494728110.0879445497707-0.2475225054920.3665946921240.1983157059590.1814380247020.0410714249679-0.2872542758970.09022513201640.136063140933-0.01720792255280.008137841085110.1725307356940.0218025767330.199551953089-5.5326918794538.083965631418.9278696071
66.03577753944-2.52468463111.510099669952.17142640886-8.845593927666.19518002904-0.25875246235-0.3523377248430.2867189792320.118463237685-0.0188251136899-0.3618027070460.397602069280.3986572529970.1065543110790.2524254867070.0695939205943-0.002395298725260.233333312772-0.04278658082750.1960185412269.4669074910730.241501351720.4402161018
76.093251327525.930558154647.94861687557.188729476649.41385224452.095377400621.32629223544-0.855697045347-0.5156207697570.532447902068-0.6358607907620.04138779760572.667793008640.432300601847-0.7359422955980.8991630203290.09966171298150.03754430839870.22494270864-0.002346399287910.2938124554215.7764084562921.00041990923.0852187778
86.55596449971-6.107802401874.04222706378.79245647283-5.068846943177.06810782890.0190815889687-0.0473713670067-0.282847229859-0.1541277625240.04789822908040.2250401313680.557477399001-0.299170828782-0.0756966149170.171133961538-0.03568261989450.04334946709880.185367890869-0.04354065943730.191269186152-2.187769043930.881985494712.1184686087
95.73577482948-4.377852737950.8978733798053.11128116415-1.992551097215.378009056440.109954963020.1515247271-0.373307819282-0.324746361849-0.06029289467210.2578458237670.6743072775230.0945243675342-0.07124029617130.196578535388-0.019323529075-0.008904991685710.191588158595-0.02258756585610.1817358411414.1044227678130.37208783294.59425773505
102.15569486627-1.38942676251-9.410583863912.026703390042.178106611587.18784570428-0.0344790713788-0.301348888105-1.561391856730.631880830853-0.6417800993860.3137865585340.348392071674-0.6654339647840.5566292399520.494882661997-0.0115917839773-0.09622135405640.2939095883260.01127735385150.54687581192710.048138102811.026569656614.1342179187
114.06249314248-3.53508388851-4.943733929013.077487085384.302030283286.019973508840.279902611546-0.5203351248690.276244026727-0.1631828249290.212717754257-0.358853392432-0.3247379257421.36796273693-0.7850432040870.6131398405140.0758913616787-0.1144665005760.275964944843-0.2300318435260.814488086146.7815436320678.745517191517.4143261109
126.289905475134.139045131740.6843715771112.120788656084.718673770365.80315619954-0.0506103476559-0.7223491938380.6625599128690.708721130823-0.48266653841.39224352189-0.254789502801-0.5260262957180.4656024997660.3872777609440.1243912343240.04283345269870.35254639975-0.05965919952670.600746476081-1.3190838151769.443574832915.3678031922
132.631792033440.5190351844028.423714290039.51727611090.3841725371296.701462482850.116179910359-0.4006530393990.3643660274350.0406321767897-0.09708011807290.386858274660.459694506513-0.238139384490.01646127387960.1744878430330.01670401295470.06956678775680.2808784592420.01199588282770.1922284820972.2771653250754.049230828310.9141391263
142.429743045051.878536681751.097101097815.68362238356-3.695280490565.45069718292-0.0184773793213-0.04264252613960.1368487649720.03839101019850.1512293053730.128668725034-0.0870091985578-0.10995544097-0.1410305390040.1171193662770.0188903768331-0.007483336178220.17422765292-0.01488272096040.23993910676615.950557467745.6792557812.8738322258
156.5607224036-1.884496383851.878650002322.326162192072.174853268676.554170811380.127214234369-0.2329448666781.10401953358-0.6691110655710.144072119163-0.79964174421-0.3600989331540.737046092882-0.3145828215780.207334021041-0.0338918227970.07945583072630.2509972581620.01513798267810.40401329359618.488404481156.07547425419.66279918582
166.088314384851.898984984542.408666079712.151041332554.252953125842.31910179408-0.0967654375561-0.5859961335280.3221956585980.4968402313510.1361665531720.444041891263-0.324371539185-0.01052107075060.02176448638210.2484849184750.0296313709870.0194381818480.285625968538-0.03193443649790.3301686668047.3712053790764.354885579518.5289778969
176.63345204656-2.227353149874.761013628472.024412924641.877512032879.89397150602-0.335694485658-0.3242377620880.8140889947071.282844613810.0896892885602-0.372907710835-1.545840302241.23061558970.0516245944050.652096213429-0.029367996587-0.1453617494220.290102251756-0.1103326303860.74201620281711.122578920173.96004262216.7988446214
183.26478732405-3.65491786672-0.6915294087512.599126286975.252828850434.60870657863-0.04408082110740.2094585962150.756807880071-0.6796314290570.164985250409-0.545736637745-0.5063132185880.205126532585-0.1553751052350.249203581467-0.0351781915740.06599827385960.2851032515130.04468206650710.40667325458411.521917720262.18856785195.29622340429
197.20429544448-4.69483722346-0.4803688461312.902826375784.149397799225.343501869150.1348474377370.4173789801470.781556716336-0.6520806304990.01142615562650.0567242232716-0.569385202634-0.296726799885-0.1175733447280.272115468069-0.002916098976760.05709830267140.2947252026750.1361104243350.4073485070552.0060545369661.93118610512.72478495379
206.28043744945-6.690834115941.522774599339.86067171543-5.203360844915.03090195375-0.234364252865-0.541368548971-0.0621243535158-0.6373375952090.695710599562-0.326110371529-0.2125681641840.430765253185-0.7017992207620.4978570078270.03626702307740.08610658883830.286321158583-0.07350990225980.7903166264071.3640889930682.677556017911.5066980019
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 127 through 129)AA127 - 1291 - 3
22chain 'A' and (resid 130 through 145)AA130 - 1454 - 19
33chain 'A' and (resid 146 through 155)AA146 - 15520 - 29
44chain 'A' and (resid 156 through 165)AA156 - 16530 - 39
55chain 'A' and (resid 166 through 175)AA166 - 17540 - 49
66chain 'A' and (resid 176 through 184)AA176 - 18450 - 58
77chain 'A' and (resid 185 through 190)AA185 - 19059 - 64
88chain 'A' and (resid 191 through 211)AA191 - 21165 - 85
99chain 'A' and (resid 212 through 232)AA212 - 23286 - 106
1010chain 'A' and (resid 233 through 237)AA233 - 237107 - 111
1111chain 'B' and (resid 127 through 129)BD127 - 1291 - 3
1212chain 'B' and (resid 130 through 145)BD130 - 1454 - 19
1313chain 'B' and (resid 146 through 155)BD146 - 15520 - 29
1414chain 'B' and (resid 156 through 165)BD156 - 16530 - 39
1515chain 'B' and (resid 166 through 175)BD166 - 17540 - 49
1616chain 'B' and (resid 176 through 184)BD176 - 18450 - 58
1717chain 'B' and (resid 185 through 190)BD185 - 19059 - 64
1818chain 'B' and (resid 191 through 211)BD191 - 21165 - 85
1919chain 'B' and (resid 212 through 232)BD212 - 23286 - 106
2020chain 'B' and (resid 233 through 237)BD233 - 237107 - 111

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