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- PDB-7amc: SmBRD3(2), Bromodomain 2 of the Bromodomain 3 protein from Schist... -

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Basic information

Entry
Database: PDB / ID: 7amc
TitleSmBRD3(2), Bromodomain 2 of the Bromodomain 3 protein from Schistosoma mansoni in complex with iBET726
ComponentsPutative bromodomain-containing protein 3, brd3
KeywordsPROTEIN BINDING / bromo domain / methyllysine binding / epigenetic reader domain / inhibitor / complex
Function / homology
Function and homology information


chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain ...Brdt, bromodomain, repeat I / 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
Chem-73B / Putative bromodomain-containing protein 3, brd3
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å
AuthorsSchiedel, M. / McDonough, M.A. / Conway, S.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHI 1408/1-1 Germany
CitationJournal: To Be Published
Title: SBM3, Bromodomain 3 from Schistosoma mansoni in complex with iBET726
Authors: Schiedel, M. / McArdle, D.J.B. / McDonough, M.A. / Conway, S.J.
History
DepositionOct 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative bromodomain-containing protein 3, brd3
B: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2388
Polymers30,0602
Non-polymers1,1786
Water6,035335
1
A: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5894
Polymers15,0301
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6494
Polymers15,0301
Non-polymers6193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.801, 83.250, 126.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

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Components

#1: Protein Putative bromodomain-containing protein 3, brd3


Mass: 15029.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5K4EQL3
#2: Chemical ChemComp-73B / 4-[(2S,4R)-1-acetyl-4-[(4-chlorophenyl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl]benzoic acid


Mass: 434.915 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium dihydrogen Phosphate monohydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97862 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 1.22→43.99 Å / Num. obs: 157260 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.056 / Rrim(I) all: 0.201 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.22-1.2510.62.0516312259620.6140.662.1581.1100
5.46-43.9912.10.1751236910210.9810.0520.18212.899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
DIALS1.12.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JVL

3jvl


Resolution: 1.22→43.982 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.176 8015 5.1 %
Rwork0.1585 149245 -
obs0.1594 157260 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.74 Å2 / Biso mean: 26.1407 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.22→43.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 82 341 2272
Biso mean--29.23 35.14 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.22-1.23370.34192820.3452486498
1.2337-1.24820.31442570.32724929100
1.2482-1.26340.32852560.31325017100
1.2634-1.27940.2942760.30524897100
1.2794-1.29620.29462710.28965059100
1.2962-1.3140.2712320.27834941100
1.314-1.33280.25292140.26615083100
1.3328-1.35260.25283020.25654906100
1.3526-1.37380.27452850.2464980100
1.3738-1.39630.25092910.2364964100
1.3963-1.42040.2262420.23524923100
1.4204-1.44620.23252590.22265080100
1.4462-1.4740.2252680.20724929100
1.474-1.50410.22812620.20054946100
1.5041-1.53680.20242550.1835042100
1.5368-1.57260.20032870.17354985100
1.5726-1.61190.20492470.17144924100
1.6119-1.65550.17722710.15995029100
1.6555-1.70420.18312740.15934987100
1.7042-1.75920.18022680.15684971100
1.7592-1.82210.18322800.15724958100
1.8221-1.89510.17272710.1535006100
1.8951-1.98130.18782700.1474964100
1.9813-2.08580.15733050.14134921100
2.0858-2.21640.13863200.13334949100
2.2164-2.38760.14532730.13554975100
2.3876-2.62780.15732020.12795022100
2.6278-3.0080.1372620.13495013100
3.008-3.78940.16922650.13265006100
3.7894-43.9820.15972680.15244975100
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)
13.5223-2.2531-3.57696.83163.12893.99810.0206-0.05450.2102-0.06830.1484-0.6693-0.36710.8373-0.21310.1793-0.07870.01680.29790.00320.248443.167372.95638.2576
27.74992.45651.30286.96391.61734.8110.0979-0.66380.86330.3487-0.1839-0.0079-0.66120.28040.04190.2611-0.0668-0.0080.2028-0.07510.226331.804778.12950.5102
34.89484.7267-5.23634.7407-4.80035.91390.1305-0.4141-0.39490.3197-0.2469-0.28910.0370.38630.17870.15020.0139-0.00870.19220.00840.169727.394864.919452.0396
45.59450.2776-2.86140.6463-0.10233.6501-0.0782-0.0085-0.119-0.012-0.0023-0.01780.06780.04960.07640.150.0020.00350.0758-0.00080.145725.963263.369445.8955
53.9502-2.95291.5183.94890.06683.44540.09470.2003-0.1258-0.7126-0.3081-0.33210.76540.54020.39840.2215-0.00140.04210.2701-0.00060.193139.620762.698434.5462
63.47960.0133-1.70960.6204-0.18083.11870.10620.17450.2801-0.0327-0.03-0.0147-0.4061-0.0138-0.08330.1874-0.008-00.10260.01230.137426.229674.971139.3949
73.59854.1796-2.84054.8806-3.60137.163-0.08980.6507-0.3038-1.19620.1201-2.2560.00210.8497-0.22360.4333-0.14130.20250.5502-0.01160.538543.689773.873626.9407
83.27570.5786-0.75474.8228-0.11875.70380.09160.0872-0.4546-0.3928-0.09820.42740.4269-0.30430.01670.197-0.0014-0.03960.0911-0.03040.212631.340644.779745.0366
97.3918-1.57631.71129.17472.95068.69470.08150.0513-0.1392-0.06490.1903-0.5370.31650.5793-0.22490.12290.0086-0.01720.1313-0.00070.191644.654347.146756.0482
103.1473-0.1062-3.12042.22781.71054.23990.0472-0.2696-0.3120.3667-0.128-0.04520.8617-0.30230.0730.2198-0.0603-0.03480.26240.04930.210635.64146.563166.3762
111.96210.86783.13821.39751.22845.27510.0165-0.13270.10880.1118-0.14750.16790.0258-0.99140.10560.1398-0.01160.01860.3329-0.00580.160431.892354.579370.8913
122.18520.71162.7971.27391.18265.13120.0207-0.2394-0.0871-0.0743-0.06890.1251-0.0102-0.60450.07820.09320.0012-0.00170.2028-0.00370.150128.874352.021655.2806
134.14342.25694.67041.70252.7155.2167-0.07960.1141-0.0521-0.08610.0805-0.1036-0.3620.24110.00540.19160.00330.00340.15030.01190.175340.582157.926253.5917
143.9124-0.36013.73166.3498-1.16243.84090.11680.4731-0.2277-0.5497-0.02630.68090.1084-0.5941-0.0820.31120.0185-0.09550.2864-0.04280.270223.667851.675538.5678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 31 )A15 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 43 )A32 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 48 )A44 - 48
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 75 )A49 - 75
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 81 )A76 - 81
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 123 )A82 - 123
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 129 )A124 - 129
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 31 )B15 - 31
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 43 )B32 - 43
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 48 )B44 - 48
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 66 )B49 - 66
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 100 )B67 - 100
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 123 )B101 - 123
14X-RAY DIFFRACTION14chain 'B' and (resid 124 through 129 )B124 - 129

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