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- PDB-7fhj: Crystal structure of BAZ2A with DNA -

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Basic information

Entry
Database: PDB / ID: 7fhj
TitleCrystal structure of BAZ2A with DNA
Components
  • Bromodomain adjacent to zinc finger domain protein 2A
  • DNA (5'-D(*CP*GP*GP*AP*AP*TP*GP*TP*AP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*TP*TP*CP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / MBD / TAM / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / 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 / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLiu, K. / Dong, A. / Li, Y. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis of the TAM domain of BAZ2A in binding to DNA or RNA independent of methylation status.
Authors: Chen, S. / Zhou, M. / Dong, A. / Loppnau, P. / Wang, M. / Min, J. / Liu, K.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 2A
B: Bromodomain adjacent to zinc finger domain protein 2A
C: DNA (5'-D(*CP*GP*GP*AP*AP*TP*GP*TP*AP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*TP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)35,29216
Polymers35,2924
Non-polymers012
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.140, 72.140, 259.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / TTF-I-interacting protein 5 / Tip5 / hWALp3


Mass: 13975.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9
#2: DNA chain DNA (5'-D(*CP*GP*GP*AP*AP*TP*GP*TP*AP*GP*GP*C)-3')


Mass: 3727.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*TP*TP*CP*CP*G)-3')


Mass: 3612.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978565 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.28→39.87 Å / Num. obs: 19242 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.02 / Rrim(I) all: 0.089 / Net I/σ(I): 23.8
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 21.3 % / Rmerge(I) obs: 1.119 / Num. unique obs: 1821 / CC1/2: 0.891 / Rpim(I) all: 0.247 / Rrim(I) all: 1.119 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
REFMAC5.8.0257refinement
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2I

3c2i


Resolution: 2.28→36.07 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.346 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 940 5.3 %RANDOM
Rwork0.2182 ---
obs0.2197 16945 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.99 Å2 / Biso mean: 39.31 Å2 / Biso min: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.28→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 487 12 24 2273
Biso mean--27.84 32.63 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181930
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.553321
X-RAY DIFFRACTIONr_angle_other_deg1.3341.7814465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.94719.052116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33715302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.931524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
LS refinement shellResolution: 2.28→2.336 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.504 14 -
Rwork0.292 1360 -
obs--99.35 %

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