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- PDB-8bpt: Crystal structure of the second bromodomain of BRD5 from Leishman... -

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Basic information

Entry
Database: PDB / ID: 8bpt
TitleCrystal structure of the second bromodomain of BRD5 from Leishmania donovani
ComponentsBromo domain-containing protein
KeywordsTRANSCRIPTION / Leishmaniasis / General Transcription / Lysine acetylation
Function / homology: / Bromodomain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Bromodomain family protein
Function and homology information
Biological speciesLeishmania donovani BPK282A1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWilkinson, A.J. / Dodson, E.J. / Jones, N.G. / Borgia, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P027989/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)White Rose DTP United Kingdom
Citation
Journal: Acs Infect Dis. / Year: 2023
Title: Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery.
Authors: Russell, C.N. / Carter, J.L. / Borgia, J.M. / Bush, J. / Calderon, F. / Gabarro, R. / Conway, S.J. / Mottram, J.C. / Wilkinson, A.J. / Jones, N.G.
#1: Journal: Biorxiv / Year: 2023
Title: Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery
Authors: Russell, C.N. / Carter, J.L. / Borgia, J.M. / Bush, J. / Calderon, F. / Gabarro, R. / Conway, S.J. / Mottram, J.C. / Wilkinson, A.J. / Jones, N.G.
#2: Journal: Nat Commun / Year: 2022
Title: Bromodomain factor 5 is an essential regulator of transcription in Leishmania.
Authors: Jones, N.G. / Geoghegan, V. / Moore, G. / Carnielli, J.B.T. / Newling, K. / Calderon, F. / Gabarro, R. / Martin, J. / Prinjha, R.K. / Rioja, I. / Wilkinson, A.J. / Mottram, J.C.
History
DepositionNov 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromo domain-containing protein
B: Bromo domain-containing protein


Theoretical massNumber of molelcules
Total (without water)31,6602
Polymers31,6602
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-7 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.370, 75.356, 105.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromo domain-containing protein


Mass: 15829.970 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani BPK282A1 (eukaryote)
Gene: LDBPK_091320 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E9BA17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→31.845 Å / Num. obs: 35399 / % possible obs: 98.3 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Net I/σ(I): 19.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.62-31.826.80.0292730.9990.0150.033
1.6-1.638.40.56817380.9280.3040.646

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
Aimlessdata scaling
xia2data reduction
pointlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TCK

5tck


Resolution: 1.6→31.845 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.487 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2147 1701 4.811 %
Rwork0.1615 33657 -
all0.164 --
obs-35358 97.893 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.081 Å2
Baniso -1Baniso -2Baniso -3
1-2.076 Å2-0 Å2-0 Å2
2---2.183 Å2-0 Å2
3---0.107 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 0 163 2375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122252
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162046
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.6553048
X-RAY DIFFRACTIONr_angle_other_deg0.4931.5564738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6945276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.057532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85510378
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.43610112
X-RAY DIFFRACTIONr_chiral_restr0.0680.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
X-RAY DIFFRACTIONr_nbd_refined0.2290.2454
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21867
X-RAY DIFFRACTIONr_nbtor_refined0.180.21163
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1220.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.780.223
X-RAY DIFFRACTIONr_nbd_other0.3860.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.218
X-RAY DIFFRACTIONr_mcbond_it2.771.6141110
X-RAY DIFFRACTIONr_mcbond_other2.7681.6141110
X-RAY DIFFRACTIONr_mcangle_it3.2782.4191384
X-RAY DIFFRACTIONr_mcangle_other3.2772.421385
X-RAY DIFFRACTIONr_scbond_it3.9511.9521142
X-RAY DIFFRACTIONr_scbond_other3.9451.951141
X-RAY DIFFRACTIONr_scangle_it4.3712.8171664
X-RAY DIFFRACTIONr_scangle_other4.372.8181665
X-RAY DIFFRACTIONr_lrange_it4.15328.432582
X-RAY DIFFRACTIONr_lrange_other4.1326.592559
X-RAY DIFFRACTIONr_rigid_bond_restr4.15434298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6410.2271100.19623940.19725980.9660.96996.38180.176
1.641-1.6860.241320.17123490.17525610.9640.97896.87620.153
1.686-1.7350.2451000.17923300.18225040.960.97797.04470.159
1.735-1.7880.241040.16422360.16824090.960.98197.13570.143
1.788-1.8470.2381140.14421800.14923580.9670.98697.28580.126
1.847-1.9110.2271150.14420820.14822530.9650.98697.51440.125
1.911-1.9830.217940.14920560.15222080.9710.98697.37320.132
1.983-2.0640.209940.13619870.13921190.9740.98998.20670.125
2.064-2.1550.203990.13718880.1420340.9740.98997.68930.127
2.155-2.260.177990.14218080.14419330.9830.98998.65490.132
2.26-2.3810.188950.13817590.14118880.980.98898.19920.132
2.381-2.5250.224910.1516420.15417610.970.98698.410.145
2.525-2.6980.231840.17115510.17416550.9640.98298.79150.171
2.698-2.9130.195830.17314700.17515690.9720.98298.98020.179
2.913-3.1880.276760.18513510.18914390.9580.97999.16610.193
3.188-3.560.181620.17112500.17213200.9790.98299.39390.186
3.56-4.1020.213460.15411280.15611800.9730.98599.49150.177
4.102-5.0030.206440.1569650.15810140.9760.98799.50690.185
5.003-6.990.223330.2037620.2038040.9780.9898.88060.231
6.99-31.8450.213260.1644690.1665060.9780.98197.82610.205
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)
10.67110.0473-0.22843.66230.03950.5024-0.008-0.06010.09030.15340.01860.0336-0.186-0.0789-0.01050.10870.0328-0.02210.09060.00610.0251-1.369918.0973-15.7546
21.6373-0.0694-0.13991.62920.5393.5095-0.00720.05360.0001-0.1150.0015-0.06930.06670.07260.00560.01350.00580.01090.01120.01040.0161-0.468347.98395.5985
Refinement TLS groupSelection: ALL

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