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- PDB-7feo: Crystal structure of AtMBD5 MBD domain -

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Basic information

Entry
Database: PDB / ID: 7feo
TitleCrystal structure of AtMBD5 MBD domain
ComponentsMethyl-CpG-binding domain-containing protein 5
KeywordsDNA BINDING PROTEIN / MBD domain / Arabidopsis thaliana / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


perinucleolar chromocenter / methyl-CpG binding / heterochromatin / enzyme binding / nucleus
Similarity search - Function
Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
Similarity search - Domain/homology
Methyl-CpG-binding domain-containing protein 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, M.Q. / Wu, Z.B. / Liu, K. / Min, J.R. / Structural Genomics Consortium (SGC)
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 21, 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

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Assembly

Deposited unit
A: Methyl-CpG-binding domain-containing protein 5
B: Methyl-CpG-binding domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7485
Polymers16,4602
Non-polymers2883
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-13 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.852, 72.852, 120.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21B-201-

HOH

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Components

#1: Protein Methyl-CpG-binding domain-containing protein 5 / AtMBD5 / MBD05 / Methyl-CpG-binding protein MBD5


Mass: 8230.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MBD5, At3g46580, F12A12.100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SNC0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M ammonium sulphate, 0.2M Sodium Chloride, 0.1M cacodylate pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→36.45 Å / Num. obs: 8605 / % possible obs: 99.91 % / Redundancy: 14.3 % / CC1/2: 1 / Net I/σ(I): 29.76
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 854 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c1t

6c1t


Resolution: 2.2→36.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.884 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 832 9.7 %RANDOM
Rwork0.2332 ---
obs0.2365 7774 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: 138.73 Å2 / Biso mean: 68.658 Å2 / Biso min: 32.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 2.2→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 15 12 845
Biso mean--74.74 64.54 -
Num. residues----99
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012876
X-RAY DIFFRACTIONr_bond_other_d0.0010.017773
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6731192
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5921771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0645100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.99119.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71115134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281510
X-RAY DIFFRACTIONr_chiral_restr0.0650.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 49 -
Rwork0.287 566 -
all-615 -
obs--100 %

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