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

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Basic information

Entry
Database: PDB / ID: 4nrc
TitleCrystal Structure of the bromodomain of human BAZ2B in complex with compound-3 N01186
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-2LY / Bromodomain adjacent to zinc finger domain protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMuniz, J.R.C. / Felletar, I. / Chaikuad, A. / Filippakopoulos, P. / Ferguson, F.M. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Muniz, J.R.C. / Felletar, I. / Chaikuad, A. / Filippakopoulos, P. / Ferguson, F.M. / Fedorov, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Ciulli, A. / 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

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)15,4725
Polymers13,6191
Non-polymers1,8534
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 96.590, 57.740
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-2159-

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-2LY / N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide


Mass: 199.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500 / Polyethylene glycol


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 7.5
Details: 19% PEG 1000, 12% glycerol, pH 7.5, 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: Jan 30, 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: 1.86→29.93 Å / Num. all: 19460 / Num. obs: 19430 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.7
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 5 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / Num. unique all: 2788 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G0L

3g0l


Resolution: 1.86→28.87 Å / Cor.coef. Fo:Fc: 0.9462 / Cor.coef. Fo:Fc free: 0.9441 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 995 5.12 %RANDOM
Rwork0.1726 ---
obs0.1735 19430 --
all-19460 --
Displacement parametersBiso mean: 30.66 Å2
Baniso -1Baniso -2Baniso -3
1--5.3483 Å20 Å20 Å2
2--2.4002 Å20 Å2
3---2.9482 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.86→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 34 231 1187
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011008HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.871356HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d477SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes147HARMONIC5
X-RAY DIFFRACTIONt_it1008HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion2.57
X-RAY DIFFRACTIONt_chiral_improper_torsion126SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1421SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.96 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2454 149 5.35 %
Rwork0.2254 2637 -
all0.2264 2786 -
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)
10.6246-0.7225-0.01294.1242.542300.0041-0.1353-0.1052-0.17860.030.0307-0.0336-0.1824-0.03410.0178-0.0404-0.03230.06140.0356-0.03597.9174-32.8768-11.0093
21.6686-0.1386-0.21061.58410.34081.57630.0019-0.0229-0.16060.0646-0.05940.11990.1035-0.05420.0574-0.0049-0.007-0.0186-0.06550.0044-0.07-21.773-25.4348-2.4649
302.7465-0.69241.27540.17420.30460.0232-0.01020.0525-0.1472-0.03860.2472-0.1322-0.04160.01540.10350.0293-0.0089-0.065-0.00930.0193-26.0999-2.0947-6.2462
40.0046-0.73531.85060.3694-0.86130.71960.009-0.0146-0.00390.01390.0246-0.0127-0.05980.0109-0.03360.0935-0.02150.04-0.066-0.0150.0004-17.3512-5.811-6.3202
50.4847-0.2805-0.45291.36090.54922.38260.0086-0.0304-0.01250.03990.0031-0.0022-0.03110.064-0.01170.00170.0021-0.0115-0.05720.0068-0.0701-18.7626-17.4962-1.1184
600.36270.47580.55081.25390.9264-0.0023-0.03060.040.12220.0304-0.05280.09860.1881-0.02810.23790.1436-0.04990.03270.0154-0.1035-12.3429-29.28463.5044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1856 - A|1863 }A1856 - 1863
2X-RAY DIFFRACTION2{ A|1864 - A|1894 }A1864 - 1894
3X-RAY DIFFRACTION3{ A|1895 - A|1903 }A1895 - 1903
4X-RAY DIFFRACTION4{ A|1904 - A|1908 }A1904 - 1908
5X-RAY DIFFRACTION5{ A|1909 - A|1961 }A1909 - 1961
6X-RAY DIFFRACTION6{ A|1962 - A|1970 }A1962 - 1970

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