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- PDB-7mwl: The TAM domain of BAZ2A in complex with a 12mer mCG DNA -

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Basic information

Entry
Database: PDB / ID: 7mwl
TitleThe TAM domain of BAZ2A in complex with a 12mer mCG DNA
Components
  • Bromodomain adjacent to zinc finger domain protein 2A
  • DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / MBD / TAM / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : ...NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : / heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / DNA binding / RNA binding / metal 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 / Bromodomain profile. / bromo domain / Bromodomain / 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: 1.84 Å
AuthorsLiu, K. / Dong, A. / Li, Y. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: The TAM domain of BAZ2A in complex with a 12mer mCG DNA
Authors: Liu, K. / Dong, A. / Li, Y. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 2A
B: Bromodomain adjacent to zinc finger domain protein 2A
E: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3995
Polymers35,3074
Non-polymers921
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.202, 73.202, 262.068
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(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')


Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.15 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 3350, 0.2M L-Proline, 0.1M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979176 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.84→37.44 Å / Num. obs: 37208 / % possible obs: 99.9 % / Redundancy: 35.5 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.008 / Rrim(I) all: 0.05 / Net I/σ(I): 48.5 / Num. measured all: 1321725 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.84-1.88200.9513.822090.8720.2140.97699.1
9.02-37.4427.10.0264240.9980.0050.02799

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.32data scaling
XDSdata processing
Aimlessphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2I

3c2i


Resolution: 1.84→36.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.389 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1855 5 %RANDOM
Rwork0.2127 ---
obs0.2135 35244 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.22 Å2 / Biso mean: 38.927 Å2 / Biso min: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.25 Å2-0 Å2
2---0.5 Å20 Å2
3---1.63 Å2
Refinement stepCycle: final / Resolution: 1.84→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 488 6 133 2389
Biso mean--56.27 42.58 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122376
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181938
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.5673312
X-RAY DIFFRACTIONr_angle_other_deg1.2711.7774495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.73119.652115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38915310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3961525
X-RAY DIFFRACTIONr_chiral_restr0.0650.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
LS refinement shellResolution: 1.842→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 131 -
Rwork0.271 2503 -
all-2634 -
obs--99.25 %
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)
14.42830.2601-0.08052.3814-0.76344.4610.1079-0.1345-0.25570.0006-0.0380.21490.0802-0.2723-0.06990.01930.01430.00390.07130.02390.0453-7.315317.31673.0591
23.0646-1.21290.21792.99140.61774.86290.17820.0934-0.0013-0.0963-0.007-0.33220.05080.2019-0.17130.01850.01840.00840.05860.01060.052514.321315.37012.8355
37.9724-1.11232.76651.47330.07561.8007-0.13390.1080.0155-0.1051-0.01920.0523-0.1292-0.11270.15310.1712-0.01930.02160.23430.03450.28174.1638.8068-2.4962
43.30940.83021.17090.55080.12680.5043-0.07990.0978-0.1229-0.05920.092-0.0359-0.033-0.0157-0.01210.10710.0115-0.01040.25310.0090.17613.756440.0938-2.0751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A543 - 701
2X-RAY DIFFRACTION2B546 - 650
3X-RAY DIFFRACTION3E1 - 12
4X-RAY DIFFRACTION4F1 - 12

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