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- PDB-4rvr: Crystal Structure of the bromodomain of human BAZ2B in complex WI... -

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Basic information

Entry
Database: PDB / ID: 4rvr
TitleCrystal Structure of the bromodomain of human BAZ2B in complex WITH GSK2801
ComponentsBromodomain adjacent to zinc finger domain protein 2B
KeywordsTRANSCRIPTION / SGC / Structural Genomics Consortium / acetylated lysine binding protein / KIAA1476 / WALp4 / chemical probe
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-3WQ / 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. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Chaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / 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
DepositionNov 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 2, 2015Group: Database references
Revision 1.4Mar 16, 2016Group: Database references
Revision 1.5Sep 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)14,3638
Polymers13,6191
Non-polymers7447
Water3,171176
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.720, 96.975, 58.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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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: Bromo domain 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-3WQ / 1-{1-[2-(methylsulfonyl)phenyl]-7-propoxyindolizin-3-yl}ethanone


Mass: 371.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21NO4S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 4.27 Å3/Da / Density % sol: 71.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.5 (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: Mar 29, 2012
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→31.43 Å / Num. all: 16635 / Num. obs: 16611 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.5
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2385 / % 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: 3G0L

3g0l


Resolution: 1.98→30.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.344 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.125 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23196 841 5.1 %RANDOM
Rwork0.18686 ---
obs0.18915 15770 99.8 %-
all-16611 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.683 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--0.08 Å20 Å2
3----1.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 1.98→30.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 50 176 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021044
X-RAY DIFFRACTIONr_bond_other_d0.0010.021001
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.0191401
X-RAY DIFFRACTIONr_angle_other_deg0.7413.0062323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63424.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47415192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.825155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211127
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_mcbond_it6.1225.808478
X-RAY DIFFRACTIONr_mcbond_other6.0515.791477
X-RAY DIFFRACTIONr_mcangle_it7.97210.779599
X-RAY DIFFRACTIONr_mcangle_other7.96710.814600
X-RAY DIFFRACTIONr_scbond_it7.997.143566
X-RAY DIFFRACTIONr_scbond_other7.9857.142566
X-RAY DIFFRACTIONr_scangle_other10.50312.393800
X-RAY DIFFRACTIONr_long_range_B_refined12.49435.6961387
X-RAY DIFFRACTIONr_long_range_B_other12.49135.7411388
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 64 -
Rwork0.38 1111 -
obs--97.92 %
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)
18.43811.0174-4.06911.56960.3912.5018-0.24220.3997-0.23410.17920.1871-0.10640.2216-0.11460.05520.12160.1105-0.03170.2471-0.05270.019233.669215.738711.506
21.34520.9337-0.15781.5314-0.52710.65250.05520.0229-0.01670.0682-0.01780.018-0.1217-0.0251-0.03740.1031-0.01050.00460.07790.00740.030361.889430.763.1771
32.5302-0.7399-1.41527.4033-4.11887.3136-0.29530.3609-0.0706-0.55050.34710.40170.6128-0.3485-0.05170.1533-0.0279-0.03260.1691-0.00670.038457.747924.7288-6.9661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1856 - 1863
2X-RAY DIFFRACTION2A1864 - 1951
3X-RAY DIFFRACTION3A1952 - 1972

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