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- PDB-6dbc: Second bromodomain of Human BRD2 with a Tetrahydroquinoline analogue -

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Basic information

Entry
Database: PDB / ID: 6dbc
TitleSecond bromodomain of Human BRD2 with a Tetrahydroquinoline analogue
ComponentsBromodomain-containing protein 2BRD2
KeywordsTranscription/inhibitor / BET / BRD2 / bromodomain / Inhibitor / Complex / Transcription / Transcription-inhibitor complex
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-G3J / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsWhite, S.W. / Yun, M.
CitationJournal: To Be Published
Title: Second bromodomain of Human BRD2 with a Tetrahydroquinoline analogue
Authors: White, S.W. / Yun, M.
History
DepositionMay 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3409
Polymers13,5241
Non-polymers8158
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint17 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.394, 72.186, 31.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13524.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25440
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-G3J / 1-[(2S,4R)-4-[(2-chlorophenyl)amino]-2-methyl-6-(1H-pyrazol-3-yl)-3,4-dihydroquinolin-1(2H)-yl]ethan-1-one


Mass: 380.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21ClN4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, Potassium thicyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 57487 / % possible obs: 99.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 8.97 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Χ2: 1.083 / Net I/σ(I): 35.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.05-1.078.80.6334820.8640.2160.6680.48197.9
1.07-1.111.90.51235490.9260.1530.5340.556100
1.1-1.13130.41935070.9550.120.4360.63100
1.13-1.1613.40.34435790.970.0970.3570.702100
1.16-1.1913.50.28935510.9760.0810.30.768100
1.19-1.2313.60.25635710.9810.0720.2660.825100
1.23-1.2713.70.22435550.9850.0620.2330.86100
1.27-1.3213.70.19335500.9890.0540.20.925100
1.32-1.3813.80.16335820.9910.0450.1690.979100
1.38-1.4613.80.13935930.9940.0390.1441.037100
1.46-1.5513.90.11835800.9950.0330.1221.181100
1.55-1.67140.10335900.9960.0280.1071.385100
1.67-1.83140.08736010.9970.0240.091.444100
1.83-2.1140.07536560.9980.0210.0771.625100
2.1-2.65140.06636890.9980.0180.0681.676100
2.65-5012.70.06338520.9970.0180.0651.80999.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IG6

5ig6


Resolution: 1.05→29.723 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 10.4
RfactorNum. reflection% reflection
Rfree0.1321 2651 4.62 %
Rwork0.1275 --
obs0.1277 57429 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.98 Å2 / Biso mean: 14.4188 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.05→29.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 55 180 1181
Biso mean--17.76 28.2 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051067
X-RAY DIFFRACTIONf_angle_d0.8951435
X-RAY DIFFRACTIONf_chiral_restr0.077139
X-RAY DIFFRACTIONf_plane_restr0.006188
X-RAY DIFFRACTIONf_dihedral_angle_d3.851866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0492-1.06820.21951320.19912725285795
1.0682-1.08880.14631380.144628452983100
1.0888-1.1110.15481370.128628542991100
1.111-1.13520.14031370.119628282965100
1.1352-1.16160.12041380.110528813019100
1.1616-1.19060.12531400.101828693009100
1.1906-1.22280.10391380.100528362974100
1.2228-1.25880.10941390.10328592998100
1.2588-1.29940.12171380.10328612999100
1.2994-1.34590.12111390.104428653004100
1.3459-1.39980.11961390.103828803019100
1.3998-1.46350.1311400.107729053045100
1.4635-1.54060.11771400.103228582998100
1.5406-1.63710.11741400.105228983038100
1.6371-1.76350.11441410.11629013042100
1.7635-1.9410.13331390.129629063045100
1.941-2.22170.12971420.126529333075100
2.2217-2.79880.15061440.144729773121100
2.7988-29.7350.13721500.153097324799

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