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- PDB-4ir3: Crystal Structure of the bromodomain of human BAZ2B in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4ir3
TitleCrystal Structure of the bromodomain of human BAZ2B in complex with 1-[7-amino-1-(pyrimidin-2-yl)indolizin-3-yl]ethanone (GSK2833282A)
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 / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
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-1FK / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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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)14,2417
Polymers13,6191
Non-polymers6236
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.100, 96.420, 57.710
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-2170-

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1FK / 1-[7-amino-1-(pyrimidin-2-yl)indolizin-3-yl]ethanone


Mass: 252.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 1000, 17% glycerol, 0.1M HEPES pH 7.0 (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: Sep 23, 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: 2→29.51 Å / Num. all: 15860 / Num. obs: 15847 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2283 / % possible all: 100

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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: 2→27.48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.089 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 790 5 %RANDOM
Rwork0.20953 ---
obs0.21126 15057 99.95 %-
all-15847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.986 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å2-0 Å2
2---0.82 Å2-0 Å2
3----1.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 43 146 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021010
X-RAY DIFFRACTIONr_bond_other_d0.0010.02961
X-RAY DIFFRACTIONr_angle_refined_deg1.5932.0041352
X-RAY DIFFRACTIONr_angle_other_deg0.78532226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49224.54544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31115183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.697155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02215
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 56 -
Rwork0.273 1103 -
obs--100 %
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)
119.9069-1.66986.09950.1979-0.50751.8731-0.2327-0.44261.38640.1174-0.1418-0.1656-0.0315-0.11920.37450.3081-0.1694-0.0430.6315-0.08970.3166-4.171633.2294-9.5254
23.9154-1.6870.6043.9444-0.92053.015-0.0174-0.01770.18440.080.0157-0.18530.0663-0.05910.00170.0054-0.0012-0.00420.0027-0.00030.013220.669117.4054-1.9542
32.00294.1715.717620.25522.821823.4677-0.0138-0.22410.24021.098-0.00471.2964-0.9122-1.00330.01860.20410.1102-0.01320.172-0.02480.25811.500530.00073.3907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1856 - 1866
2X-RAY DIFFRACTION2A1867 - 1963
3X-RAY DIFFRACTION3A1964 - 1971

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