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- PDB-7l9j: Crystal structure of the second bromodomain (BD2) of human BRD2 b... -

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Basic information

Entry
Database: PDB / ID: 7l9j
TitleCrystal structure of the second bromodomain (BD2) of human BRD2 bound to Ro3280
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / 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-79C / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKarim, M.R. / Bikowitz, M.J. / 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 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)13,9543
Polymers13,3751
Non-polymers5792
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bromodomain-containing protein 2
hetero molecules

A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9096
Polymers26,7512
Non-polymers1,1584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1690 Å2
ΔGint-18 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.330, 72.148, 31.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-502-

CL

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13375.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-79C / 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 543.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35F2N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 10855 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.03 / Rrim(I) all: 0.073 / Χ2: 0.876 / Net I/σ(I): 10.4 / Num. measured all: 62931
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.884.80.2585200.9440.1270.2890.53396.8
1.88-1.925.60.2295160.9680.1050.2520.774100
1.92-1.955.80.2075330.9740.0950.2280.597100
1.95-1.995.90.1765410.9770.080.1940.603100
1.99-2.045.90.1525220.9880.0680.1670.626100
2.04-2.085.90.1425250.9880.0640.1560.628100
2.08-2.145.80.1245410.9860.0560.1360.695100
2.14-2.1960.115470.9930.0490.1210.699100
2.19-2.2660.1055240.9920.0470.1150.69100
2.26-2.335.90.0925270.9930.0420.1010.759100
2.33-2.415.90.0945390.9950.0420.1040.771100
2.41-2.515.90.0855380.9930.0380.0930.784100
2.51-2.6360.0725470.9960.0320.0790.826100
2.63-2.765.90.075330.9960.0310.0770.836100
2.76-2.945.90.0615550.9970.0270.0670.884100
2.94-3.1660.0565420.9970.0250.0621.05100
3.16-3.485.90.0455490.9980.020.0491.077100
3.48-3.995.90.0425670.9980.0190.0461.416100
3.99-5.025.80.045650.9980.0180.0441.49100
5.02-505.20.0416240.9980.020.0451.62899.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9G

7l9g


Resolution: 1.85→42.361 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 542 5.01 %
Rwork0.1619 10281 -
obs0.1641 10823 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.83 Å2 / Biso mean: 16.6943 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: final / Resolution: 1.85→42.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 40 110 1060
Biso mean--27.81 24.61 -
Num. residues----110
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8503-2.03650.2291310.1621249699
2.0365-2.33120.22511330.15442528100
2.3312-2.9370.21281350.16252569100
2.937-42.3610.18861430.16482688100
Refinement TLS params.Method: refined / Origin x: 10.4404 Å / Origin y: 2.2887 Å / Origin z: 1.1564 Å
111213212223313233
T0.0762 Å2-0.0133 Å20.005 Å2-0.1002 Å2-0.0136 Å2--0.0901 Å2
L1.0504 °2-0.5109 °20.1222 °2-2.0756 °2-0.395 °2--0.8114 °2
S0.0066 Å °-0.0144 Å °0.0327 Å °-0.0314 Å °0.0097 Å °-0.055 Å °-0.0268 Å °0.0315 Å °-0.0048 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA346 - 455
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allQ1 - 113

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