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- PDB-3aqa: Crystal structure of the human BRD2 BD1 bromodomain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3aqa
TitleCrystal structure of the human BRD2 BD1 bromodomain in complex with a BRD2-interactive compound, BIC1
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / helical bundle / acetyl-lysine recognition / acetylated histone H4 / nucleus / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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 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-BYH / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUmehara, T. / Nakamura, Y. / Terada, T. / Shirouzu, M. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Chem.Biol. / Year: 2011
Title: Real-Time Imaging of Histone H4K12-Specific Acetylation Determines the Modes of Action of Histone Deacetylase and Bromodomain Inhibitors
Authors: Ito, T. / Umehara, T. / Sasaki, K. / Nakamura, Y. / Nishino, N. / Terada, T. / Shirouzu, M. / Padmanabhan, B. / Yokoyama, S. / Ito, A. / Yoshida, M.
History
DepositionOct 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3235
Polymers45,7883
Non-polymers5362
Water1,892105
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7983
Polymers15,2631
Non-polymers5362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)15,2631
Polymers15,2631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)15,2631
Polymers15,2631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0614
Polymers30,5252
Non-polymers5362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-14 kcal/mol
Surface area12190 Å2
MethodPISA
5
C: Bromodomain-containing protein 2

C: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)30,5252
Polymers30,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2120 Å2
ΔGint-10 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.597, 55.716, 68.205
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 15262.552 Da / Num. of mol.: 3 / Fragment: residues 73-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: bacterial cell free system (unknown) / References: UniProt: P25440
#2: Chemical ChemComp-BYH / 1-[2-(1H-benzimidazol-2-ylsulfanyl)ethyl]-3-methyl-1,3-dihydro-2H-benzimidazole-2-thione


Mass: 340.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4S2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG MME 5000, 0.2M ammonium sulfate, 0.1M HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→31.45 Å / Num. all: 19170 / Num. obs: 18668 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0J

1x0j


Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 414406.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1845 9.9 %RANDOM
Rwork0.189 ---
obs0.189 18668 97.2 %-
all-19185 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7999 Å2 / ksol: 0.468621 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å2-2.4 Å2
2---0.47 Å20 Å2
3----2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 35 105 2923
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it3.092
X-RAY DIFFRACTIONc_scbond_it3.712
X-RAY DIFFRACTIONc_scangle_it4.812.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 298 10 %
Rwork0.197 2670 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2DRG_param.txtDRG_top.txt
X-RAY DIFFRACTION3mes_xplor_param.txtmes_xplor_top.txt
X-RAY DIFFRACTION4water_rep.paramwater_rep.top

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