- PDB-7oe9: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH rac-N5-((1R,5S)-3-oxabi... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7oe9
Title
C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH rac-N5-((1R,5S)-3-oxabicyclo[3.1.0]hexan-6-yl)-N7,3-dimethyl-3-phenyl-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 / 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 ...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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / 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, conserved site / Bromodomain signature. / Bromodomain ...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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54178 Å / Relative weight: 1
Reflection
Resolution: 1.6→52.45 Å / Num. obs: 14973 / % possible obs: 90.3 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.024 / Net I/σ(I): 24.1
Reflection shell
Resolution: 1.6→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1679 / CC1/2: 0.754 / % possible all: 71.5
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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 Resolution: 1.602→14.12 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.09
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2011
759
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RANDOM
Rwork
0.1778
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obs
0.179
14830
89.5 %
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Displacement parameters
Biso mean: 18.6 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.4406 Å2
0 Å2
0 Å2
2-
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0.2146 Å2
0 Å2
3-
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-1.6552 Å2
Refine analyze
Luzzati coordinate error obs: 0.19 Å
Refinement step
Cycle: LAST / Resolution: 1.602→14.12 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
910
0
37
132
1079
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
983
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.71
1328
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
355
SINUSOIDAL
2
X-RAY DIFFRACTION
t_gen_planes
179
HARMONIC
5
X-RAY DIFFRACTION
t_it
983
HARMONIC
10
X-RAY DIFFRACTION
t_chiral_improper_torsion
113
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_ideal_dist_contact
974
SEMIHARMONIC
4
X-RAY DIFFRACTION
t_omega_torsion
3.66
X-RAY DIFFRACTION
t_other_torsion
14.39
LS refinement shell
Resolution: 1.602→1.63 Å
Rfactor
Num. reflection
% reflection
Rfree
0.2326
20
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Rwork
0.23
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-
obs
-
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58.17 %
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