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- PDB-7fef: Crystal structure of AtMBD6 with DNA -

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Basic information

Entry
Database: PDB / ID: 7fef
TitleCrystal structure of AtMBD6 with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain-containing protein 6
KeywordsDNA BINDING PROTEIN/DNA / MBD / DNA-protein complex structure / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleolus organizer region / perinucleolar chromocenter / regulatory ncRNA-mediated gene silencing / methyl-CpG binding / plastid / heterochromatin / : / enzyme binding / nucleus
Similarity search - Function
Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Methyl-CpG-binding domain-containing protein 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsWu, Z.B. / Liu, K. / Min, J.R.
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs.
Authors: Wu, Z. / Chen, S. / Zhou, M. / Jia, L. / Li, Z. / Zhang, X. / Min, J. / Liu, K.
History
DepositionJul 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
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')
A: Methyl-CpG-binding domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)15,5653
Polymers15,5653
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-1 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.316, 40.316, 83.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: 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)
#2: Protein Methyl-CpG-binding domain-containing protein 6 / AtMBD6 / MBD06 / Methyl-CpG-binding protein MBD6


Mass: 8210.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MBD6, At5g59380, F2O15.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LTJ1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis-tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.29→34.91 Å / Num. obs: 6926 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 75.32 Å2 / CC1/2: 0.989 / Net I/σ(I): 12.4
Reflection shellResolution: 2.29→2.37 Å / Num. unique obs: 692 / CC1/2: 0.644 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c1a, 2yk8

6c1a

2yk8
PDB Unreleased entry


Resolution: 2.39→34.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN DADED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 303 5 %RANDOM
Rwork0.2233 ---
obs0.2248 5757 99.93 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso max: 139.46 Å2 / Biso mean: 69.3496 Å2 / Biso min: 42.86 Å2
Refinement stepCycle: final / Resolution: 2.39→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms395 488 0 20 903
Biso mean---65.73 -
Num. residues----72
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012954
X-RAY DIFFRACTIONr_bond_other_d0.0010.019629
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.4411396
X-RAY DIFFRACTIONr_angle_other_deg1.4682.2081464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.163547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.6822025
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.141559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.567154
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0840.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
LS refinement shellResolution: 2.39→2.448 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.409 21 -
Rwork0.402 402 -
obs--99.06 %

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