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

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Basic information

Entry
Database: PDB / ID: 4nra
TitleCrystal Structure of the bromodomain of human BAZ2B in complex with compound-6 E11322
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-2LW / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChaikuad, A. / Felletar, I. / Ferguson, F.M. / 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: 2013
Title: Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain.
Authors: Ferguson, F.M. / Fedorov, O. / Chaikuad, A. / Philpott, M. / Muniz, J.R. / Felletar, I. / von Delft, F. / Heightman, T. / Knapp, S. / Abell, C. / Ciulli, A.
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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)14,1787
Polymers13,6191
Non-polymers5596
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.477, 96.377, 57.705
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-2267-

HOH

21A-2268-

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 (UNP 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-2LW / 1-(8-chloro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)ethanone


Mass: 248.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13ClN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO ISOFORM 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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% low MW PEG Smears, 0.1M MES pH 6.5, 15%(v/v) glycerol, 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 22, 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: 1.85→19.52 Å / Num. all: 19728 / Num. obs: 19706 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2816 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G0L

3g0l


Resolution: 1.85→19.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.178 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21227 1007 5.1 %RANDOM
Rwork0.17725 ---
obs0.17896 18697 99.65 %-
all-19706 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.842 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å20 Å2
2---0.9 Å2-0 Å2
3----1.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 37 187 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021012
X-RAY DIFFRACTIONr_bond_other_d0.0030.02967
X-RAY DIFFRACTIONr_angle_refined_deg1.5672.0031359
X-RAY DIFFRACTIONr_angle_other_deg0.9373.0042246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18724.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81215188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.244155
X-RAY DIFFRACTIONr_chiral_restr0.090.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02215
X-RAY DIFFRACTIONr_mcbond_it4.0134.217469
X-RAY DIFFRACTIONr_mcbond_other3.994.191468
X-RAY DIFFRACTIONr_mcangle_it4.857.793586
X-RAY DIFFRACTIONr_mcangle_other4.8857.823587
X-RAY DIFFRACTIONr_scbond_it5.9215.189543
X-RAY DIFFRACTIONr_scbond_other5.9195.193544
X-RAY DIFFRACTIONr_scangle_other7.4239.067771
X-RAY DIFFRACTIONr_long_range_B_refined10.09428.1411390
X-RAY DIFFRACTIONr_long_range_B_other10.09328.1551391
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 79 -
Rwork0.307 1356 -
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)
111.573-1.3381-7.349410.02971.67444.74470.2389-1.2635-0.2029-1.0281-0.2473-0.2695-0.30520.82080.00840.34110.0614-0.06940.5766-0.20130.200632.498615.693411.2532
29.1582.5842-5.19554.1476-1.35116.5464-0.25290.1713-1.0405-0.2640.0594-0.30760.4527-0.23830.19350.0661-0.0173-0.04540.0347-0.00970.241358.714317.48972.7784
33.59611.53190.03413.9479-0.59753.6835-0.03120.01440.0751-0.01090.0674-0.1156-0.3719-0.0087-0.03610.0512-0.00730.00610.0051-0.00260.009361.540634.27982.5772
48.69742.6717-6.031710.1745-3.74928.6848-0.34790.5834-0.8746-0.64420.51440.28030.5253-0.6312-0.16660.1373-0.0777-0.0180.127-0.04260.238754.633920.5653-5.2834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1856 - 1863
2X-RAY DIFFRACTION2A1864 - 1884
3X-RAY DIFFRACTION3A1885 - 1958
4X-RAY DIFFRACTION4A1959 - 1971

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