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- PDB-7lah: Crystal structure of the first bromodomain (BD1) of human BRD2 bo... -

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Basic information

Entry
Database: PDB / ID: 7lah
TitleCrystal structure of the first bromodomain (BD1) of human BRD2 bound to bromosporine
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
Function / homology
Function and homology information


nuclear speck / nucleoplasm
Similarity search - Function
Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / : / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromosporine / PHOSPHATE ION / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKarim, M.R. / Bikowitz, M. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 24, 2021Group: 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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9713
Polymers14,4721
Non-polymers4992
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.870, 80.670, 47.680
Angle α, β, γ (deg.)90.000, 137.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-202-

PO4

21A-320-

HOH

31A-385-

HOH

41A-404-

HOH

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 14471.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: U3KQA6
#2: Chemical ChemComp-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20 % w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40.606 Å / Num. obs: 18289 / % possible obs: 95.9 % / Redundancy: 2.022 % / Biso Wilson estimate: 22.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.023 / Rrim(I) all: 0.029 / Χ2: 0.994 / Net I/σ(I): 18.55 / Num. measured all: 36983 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.641.5760.3441.512030141112880.7890.48791.3
1.64-1.691.5990.2452.042036135612730.8840.34693.9
1.69-1.741.6360.192.722068133112640.9270.26995
1.74-1.791.6730.1214.132050126612250.9710.17296.8
1.79-1.851.7030.1095.432064125412120.9730.15596.7
1.85-1.911.7370.0767.42085122412000.9860.10898
1.91-1.981.7650.05810.732023117111460.990.08397.9
1.98-2.071.7920.04513.251950112410880.9940.06496.8
2.07-2.161.8010.03416.31866107810360.9960.04896.1
2.16-2.261.8350.02919.56183310379990.9970.04196.3
2.26-2.391.8750.02621.9917799839490.9980.03796.5
2.39-2.531.9110.02325.4717089308940.9980.03396.1
2.53-2.72.0110.02228.2616738748320.9980.03195.2
2.7-2.922.1820.02231.4617308247930.9980.02996.2
2.92-3.22.4770.02137.818117537310.9990.02697.1
3.2-3.583.3290.02149.621876836570.9990.02496.2
3.58-4.133.6360.01956.4221566065930.9990.02397.9
4.13-5.063.5990.01756.1418215185060.9990.0297.7
5.06-7.163.5750.01955.2414054093930.9990.02296.1
7.16-40.6063.3710.0255.867082332100.9990.02390.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9G

7l9g


Resolution: 1.6→40.606 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 915 5 %
Rwork0.1803 17374 -
obs0.1815 18289 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.59 Å2 / Biso mean: 28.3374 Å2 / Biso min: 13.86 Å2
Refinement stepCycle: final / Resolution: 1.6→40.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 33 113 1152
Biso mean--24.53 39.41 -
Num. residues----121
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.68440.39321250.3584238293
1.6844-1.78990.30281290.2374243596
1.7899-1.92810.24011320.222252498
1.9281-2.12210.23871320.1854249398
2.1221-2.42910.21871300.1782248598
2.4291-3.06030.2121320.1849249597
3.0603-40.60.1581350.1508256099
Refinement TLS params.Method: refined / Origin x: 17.2378 Å / Origin y: -17.174 Å / Origin z: -0.9889 Å
111213212223313233
T0.1381 Å20.0179 Å20.0082 Å2-0.1777 Å20.0069 Å2--0.1321 Å2
L1.0631 °2-0.0821 °2-0.4489 °2-4.3522 °20.5264 °2--0.4893 °2
S0.1074 Å °0.0428 Å °0.0792 Å °-0.0596 Å °-0.0559 Å °0.1624 Å °-0.0609 Å °-0.0323 Å °-0.0404 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA73 - 193
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allQ1 - 115
4X-RAY DIFFRACTION1allP1

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