- PDB-7oe8: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-((1R,5S,6r)-3-oxabic... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7oe8
Title
C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-((1R,5S,6r)-3-oxabicyclo[3.1.0]hexan-6-yl)-3-(1H-indol-4-yl)-N7-methyl-2,3-dihydrobenzofuran-5,7-dicarboxamide
Components
Bromodomain-containing protein 2
Keywords
NUCLEAR PROTEIN / Inhibitor / Bromodomain
Function / homology
Function and homology information
acetylation-dependent protein binding / chromatin looping / positive regulation of T-helper 17 cell lineage commitment / RUNX3 regulates p14-ARF / protein localization to chromatin / lysine-acetylated histone binding / neural tube closure / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / positive regulation of T-helper 17 cell lineage commitment / RUNX3 regulates p14-ARF / protein localization to chromatin / lysine-acetylated histone binding / neural tube closure / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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, conserved site / Bromodomain signature. / Bromodomain profile. ...NET domain superfamily / : / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97949 Å / Relative weight: 1
Reflection
Resolution: 1.3→19.51 Å / Num. obs: 29361 / % possible obs: 96.6 % / Redundancy: 15.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.8
Reflection shell
Resolution: 1.3→1.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3570 / CC1/2: 0.924 / % possible all: 82.6
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Processing
Software
Name
Version
Classification
BUSTER
2.11.7 (6-FEB-2020)
refinement
XDS
datareduction
Aimless
datascaling
Refinement
Method to determine structure: FOURIER SYNTHESIS Starting model: in house model Resolution: 1.301→19.51 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.056
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2147
1408
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RANDOM
Rwork
0.2037
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obs
0.2042
29329
96.3 %
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Displacement parameters
Biso mean: 15.12 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.1299 Å2
0 Å2
0 Å2
2-
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1.2341 Å2
0 Å2
3-
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-3.364 Å2
Refine analyze
Luzzati coordinate error obs: 0.18 Å
Refinement step
Cycle: LAST / Resolution: 1.301→19.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
923
0
39
164
1126
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
1009
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.85
1362
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
361
SINUSOIDAL
2
X-RAY DIFFRACTION
t_gen_planes
168
HARMONIC
5
X-RAY DIFFRACTION
t_it
1009
HARMONIC
10
X-RAY DIFFRACTION
t_chiral_improper_torsion
116
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_ideal_dist_contact
1018
SEMIHARMONIC
4
X-RAY DIFFRACTION
t_omega_torsion
4.35
X-RAY DIFFRACTION
t_other_torsion
16.7
LS refinement shell
Resolution: 1.301→1.31 Å
Rfactor
Num. reflection
% reflection
Rfree
0.2212
20
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Rwork
0.2
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obs
-
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67.82 %
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