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- PDB-4ir6: Crystal Structure of the bromodomain of human BAZ2B in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4ir6
TitleCrystal Structure of the bromodomain of human BAZ2B in complex with 1-{1-[2-(METHYLSULFONYL)PHENYL]-7-PHENOXYINDOLIZIN-3-YL}ETHANONE (GSK2838097A)
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / SGC / Structural Genomics Consortium / bromodomain / acetylated lysine binding protein / KIAA1476 / WALp4
Function / homology
Function and homology information


chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus
Similarity search - Function
BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain ...BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-IR6 / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. ...Chaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B.
Authors: Chen, P. / Chaikuad, A. / Bamborough, P. / Bantscheff, M. / Bountra, C. / Chung, C.W. / Fedorov, O. / Grandi, P. / Jung, D. / Lesniak, R. / Lindon, M. / Muller, S. / Philpott, M. / Prinjha, ...Authors: Chen, P. / Chaikuad, A. / Bamborough, P. / Bantscheff, M. / Bountra, C. / Chung, C.W. / Fedorov, O. / Grandi, P. / Jung, D. / Lesniak, R. / Lindon, M. / Muller, S. / Philpott, M. / Prinjha, R. / Rogers, C. / Selenski, C. / Tallant, C. / Werner, T. / Willson, T.M. / Knapp, S. / Drewry, D.H.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 9, 2015Group: Database references
Revision 1.4Oct 21, 2015Group: Database references
Revision 1.5Apr 20, 2016Group: Database references
Revision 1.6Sep 20, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3978
Polymers13,6191
Non-polymers7787
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.120, 96.500, 57.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2273-

HOH

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9UIF8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IR6 / 1-{1-[2-(methylsulfonyl)phenyl]-7-phenoxyindolizin-3-yl}ethanone


Mass: 405.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19NO4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IN THIS ENTRY CORRESPONDS TO ISOFORM Q9UIF8-4

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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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 28% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.25 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 5, 2011
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→27.35 Å / Num. all: 21388 / Num. obs: 21365 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3070 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3G0L

3g0l


Resolution: 1.8→26.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.554 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.091 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21639 1098 5.1 %RANDOM
Rwork0.1755 ---
obs0.17752 20266 99.89 %-
all-21365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.405 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--0.19 Å20 Å2
3----1.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.213 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 53 214 1206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191037
X-RAY DIFFRACTIONr_bond_other_d0.0020.02982
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9881395
X-RAY DIFFRACTIONr_angle_other_deg0.81632279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68724.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98515191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.457155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 81 -
Rwork0.316 1460 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
114.19437.631112.19599.661410.278312.9729-0.0651-0.4970.04350.16450.4737-0.6580.09840.067-0.40860.2097-0.07830.02720.4167-0.03890.1593-7.917432.6378-11.1993
22.9363-1.01740.67363.7954-1.20622.65520.0640.034-0.0531-0.1034-0.04510.00160.175-0.0172-0.01890.0480.00370.01080.0476-0.00940.007719.978917.7069-3.2006
36.9176-5.60122.830516.0073-4.22766.5919-0.4168-0.49620.14460.56390.37110.2131-0.4117-0.45470.04570.12270.02390.01890.1248-0.02720.020215.768923.62896.6233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1856 - 1863
2X-RAY DIFFRACTION2A1864 - 1951
3X-RAY DIFFRACTION3A1952 - 1971

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