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- PDB-7amh: SmBRD3(2), Second Bromodomain of Bromodomain 3 from Schistosoma m... -

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Basic information

Entry
Database: PDB / ID: 7amh
TitleSmBRD3(2), Second Bromodomain of Bromodomain 3 from Schistosoma mansoni in complex with DM-A-33, an iBET726 analogue
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-RN5 / Putative bromodomain-containing protein 3, brd3
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.863 Å
AuthorsMcArdle, D. / Schiedel, M. / McDonough, M.A. / Conway, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S507015/1 United Kingdom
CitationJournal: To Be Published
Title: SBM3_2, Second Bromodomain of Bromodomain 3 from Schistosoma mansoni in complex with DM1, an iBET726 analogue
Authors: McArdle, D.J.B. / Schiedel, M. / 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)30,9734
Polymers30,0602
Non-polymers9132
Water3,729207
1
A: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4862
Polymers15,0301
Non-polymers4571
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)15,4862
Polymers15,0301
Non-polymers4571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.201, 84.111, 126.736
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-387-

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-RN5 / 4-{(2S, 4R)-1-acetyl-4-[(1-benzothiophen-6-yl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl}benzoic acid / 4-[(2~{S},4~{R})-4-(1-benzothiophen-6-ylamino)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-6-yl]benzoic acid


Mass: 456.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.21 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: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.863→63.368 Å / Num. obs: 42925 / % possible obs: 99.9 % / Redundancy: 11.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.069 / Rrim(I) all: 0.237 / Net I/σ(I): 6.8
Reflection shellResolution: 1.863→1.895 Å / Rmerge(I) obs: 4.369 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2292 / CC1/2: 0.47 / Rpim(I) all: 1.506 / Rrim(I) all: 4.632

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AMC

7amc


Resolution: 1.863→63.368 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2157 5.03 %
Rwork0.2174 40768 -
obs0.2191 42925 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.08 Å2 / Biso mean: 40.8409 Å2 / Biso min: 17.44 Å2
Refinement stepCycle: final / Resolution: 1.863→63.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 112 210 2143
Biso mean--37.98 40.04 -
Num. residues----226
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.863-1.90630.4317920.3752174761
1.9063-1.9540.38811150.3514231382
1.954-2.00690.33631140.3399260889
2.0069-2.06590.3571200.3202285899
2.0659-2.13260.30971650.29012792100
2.1326-2.20880.27941560.26152835100
2.2088-2.29730.30331610.2485281299
2.2973-2.40180.25541630.23152858100
2.4018-2.52850.22681580.21832839100
2.5285-2.68690.23281420.20542864100
2.6869-2.89430.25961570.20872857100
2.8943-3.18560.23591670.19982818100
3.1856-3.64650.23051230.18812872100
3.6465-4.5940.22861650.16552850100
4.594-63.3680.22051590.21092845100
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)
16.3506-1.1316-3.48238.7532.88934.35260.0262-0.26520.73690.23160.54-1.2617-0.0161.8117-0.47390.306-0.1342-0.010.6099-0.03790.486443.307473.998438.404
28.0487-3.13010.56867.3654.18223.19990.0187-0.93521.26760.51410.0984-0.8668-0.25990.6744-0.03990.4763-0.2401-0.01610.5758-0.09940.48734.092780.484350.6346
33.14481.0145-3.15554.2985-2.35398.7108-0.0476-0.1088-0.21110.10930.0475-0.11960.21170.2442-0.03410.15050.03290.00330.1879-0.0150.18922.424165.340748.5836
47.8601-1.3751-4.6411.69440.50035.28080.02510.2331-0.0979-0.1474-0.0494-0.1794-0.20370.40150.03010.2407-0.0457-0.01940.2878-0.03090.180231.506368.827138.7866
57.54432.0615-6.01582.6212-1.89478.4450.28640.33440.3912-0.2616-0.1007-0.2345-0.8745-0.1496-0.28070.4976-0.0390.01140.18160.03950.292428.382379.986639.225
67.43771.8473.02887.836-0.35162.34570.08180.6594-0.8499-0.7724-0.13060.63220.46020.060.07790.3975-0.0319-0.02350.3119-0.08020.339331.786846.117645.1033
76.78920.83291.72377.6334.48542.90370.02960.0274-0.2067-0.54690.624-0.73160.57090.6855-0.55310.3843-0.00360.00950.3035-0.01580.372745.563347.378954.3218
82.51180.78792.28212.17982.89248.88790.1572-0.0508-0.11270.1583-0.2540.20590.4441-0.73980.11050.1858-0.0775-0.00850.36850.00060.24832.846151.067365.4528
94.21231.27634.09840.98741.61128.35990.0856-0.22720.02-0.008-0.23430.2908-0.0172-0.92780.22720.21040.0567-0.02160.4178-0.02630.261629.122255.664155.1331
109.24531.86614.73155.00210.94453.56140.20440.2756-0.0472-0.2019-0.2380.095-0.13620.14250.06650.25530.04220.03820.2770.00450.238838.212357.622451.0755
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 40 )A32 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 66 )A41 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 100 )A67 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 127 )A101 - 127
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 31 )B16 - 31
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 40 )B32 - 40
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 75 )B41 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 100 )B76 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 128 )B101 - 128

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