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

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Basic information

Entry
Database: PDB / ID: 7lai
TitleCrystal structure of the first bromodomain (BD1) of human BRD2 bound to BI2536
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
Function / homology
Function and homology information


chromosome / chromatin organization / nuclear speck / nucleoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-R78 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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)14,9942
Polymers14,4721
Non-polymers5221
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.550, 81.730, 48.510
Angle α, β, γ (deg.)90.000, 138.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-344-

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-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

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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: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→33.573 Å / Num. obs: 12117 / % possible obs: 97.1 % / Redundancy: 3.558 % / Biso Wilson estimate: 29.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.031 / Χ2: 0.989 / Net I/σ(I): 25.48 / Num. measured all: 43116 / Scaling rejects: 25
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
1.85-1.92.390.2554.0720059198390.9650.32191.3
1.9-1.953.4440.2475.5429868908670.9740.29297.4
1.95-2.013.6080.177.9830528718460.9880.297.1
2.01-2.073.6240.12310.2330088508300.9930.14597.6
2.07-2.143.6470.09512.7328968097940.9960.11198.1
2.14-2.213.6390.07215.928608047860.9970.08597.8
2.21-2.293.6670.06516.9727067457380.9980.07799.1
2.29-2.393.6650.05520.2426177337140.9980.06597.4
2.39-2.493.690.04423.1425727136970.9990.05297.8
2.49-2.623.6670.0425.5424026696550.9990.04697.9
2.62-2.763.7040.03330.6623896536450.9990.03998.8
2.76-2.933.7180.02834.222316156000.9990.03397.6
2.93-3.133.7020.02537.920515605540.9990.02998.9
3.13-3.383.7030.0245.9619485345260.9990.02498.5
3.38-3.73.6950.01952.9418075024890.9990.02297.4
3.7-4.143.70.01858.3616064484340.9990.02196.9
4.14-4.783.6610.01759.71141339938610.01996.7
4.78-5.853.710.01958.9812023363240.9990.02296.4
5.85-8.273.5530.01960.539062702550.9990.02394.4
8.27-33.5733.3260.01862.5145915413810.02289.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LAH

7lah


Resolution: 1.85→33.573 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 606 5.01 %
Rwork0.1901 11493 -
obs0.1916 12099 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.51 Å2 / Biso mean: 38.6451 Å2 / Biso min: 22.79 Å2
Refinement stepCycle: final / Resolution: 1.85→33.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 38 49 1084
Biso mean--50.6 44.69 -
Num. residues----120
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-2.0360.27741470.2496279296
2.036-2.33050.29021520.2171289199
2.3305-2.93590.24771530.2137289599
2.9359-33.570.18441540.1666291599
Refinement TLS params.Method: refined / Origin x: 10.5306 Å / Origin y: -15.8806 Å / Origin z: 0.8759 Å
111213212223313233
T0.2602 Å2-0.0184 Å2-0.0089 Å2-0.2903 Å20.002 Å2--0.2325 Å2
L0.7634 °2-0.3637 °20.0576 °2-1.4312 °2-0.1459 °2--0.3685 °2
S0.0149 Å °0.0453 Å °0.0043 Å °0.0034 Å °0.0243 Å °0.0491 Å °-0.0371 Å °0.1518 Å °-0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA73 - 192
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allQ1 - 50

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