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

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Basic information

Entry
Database: PDB / ID: 4xub
TitleCrystal Structure of the bromodomain of human BAZ2B in complex with BAZ2-ICR chemical probe
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / bromodomain / acetylated lysine binding protein / KIAA1476 / WALp4 / SGC / Structural Genomics Consortium
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-43D / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChaikuad, A. / Felletar, I. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B.
Authors: Drouin, L. / McGrath, S. / Vidler, L.R. / Chaikuad, A. / Monteiro, O. / Tallant, C. / Philpott, M. / Rogers, C. / Fedorov, O. / Liu, M. / Akhtar, W. / Hayes, A. / Raynaud, F. / Muller, S. / ...Authors: Drouin, L. / McGrath, S. / Vidler, L.R. / Chaikuad, A. / Monteiro, O. / Tallant, C. / Philpott, M. / Rogers, C. / Fedorov, O. / Liu, M. / Akhtar, W. / Hayes, A. / Raynaud, F. / Muller, S. / Knapp, S. / Hoelder, S.
History
DepositionJan 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,1635
Polymers13,6191
Non-polymers5454
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint7 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.170, 96.690, 57.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: UNP residues 1858-1972
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) / Variant (production host): R3 / References: UniProt: Q9UIF8
#2: Chemical ChemComp-43D / 4-{4-(1-methyl-1H-pyrazol-4-yl)-1-[2-(4-methyl-1H-1,2,3-triazol-1-yl)ethyl]-1H-imidazol-5-yl}benzonitrile


Mass: 358.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.46 %
Crystal growTemperature: 277.14 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 34% Low Molecular Weight PEG Smears (LMW PEG smears), 0.1M MES pH 6.0 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution)

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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: Dec 12, 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: 1.98→33.22 Å / Num. obs: 16214 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

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

3g0l


Resolution: 1.98→33.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.228 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21495 814 5 %RANDOM
Rwork0.18028 ---
obs0.18199 15385 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.793 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3----1.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: 1 / Resolution: 1.98→33.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 39 165 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021017
X-RAY DIFFRACTIONr_bond_other_d0.0020.02971
X-RAY DIFFRACTIONr_angle_refined_deg1.5432.0221366
X-RAY DIFFRACTIONr_angle_other_deg0.8313.0062252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56124.54544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58715188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.731155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7492.555467
X-RAY DIFFRACTIONr_mcbond_other1.7492.545466
X-RAY DIFFRACTIONr_mcangle_it2.7273.81583
X-RAY DIFFRACTIONr_mcangle_other2.7253.822584
X-RAY DIFFRACTIONr_scbond_it2.132.885550
X-RAY DIFFRACTIONr_scbond_other2.1142.885550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2324.174782
X-RAY DIFFRACTIONr_long_range_B_refined8.23123.8061357
X-RAY DIFFRACTIONr_long_range_B_other8.22823.8421358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 63 -
Rwork0.308 1110 -
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)
122.8679-10.2117-20.08622.132419.510923.97-0.2703-0.013-0.4904-0.46920.5997-1.0704-0.14830.3778-0.32940.28360.1287-0.1160.4947-0.07730.271232.656515.073711.0494
25.03912.1002-0.39465.0668-0.92554.5596-0.04150.1229-0.2968-0.17370.0544-0.1062-0.14-0.1625-0.01280.0589-0.0039-0.0050.0527-0.00530.019259.75529.42661.4525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1856 - 1863
2X-RAY DIFFRACTION2A1864 - 1971

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