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- PDB-4e9e: Structure of the glycosylase domain of MBD4 -

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Basic information

Entry
Database: PDB / ID: 4e9e
TitleStructure of the glycosylase domain of MBD4
ComponentsMethyl-CpG-binding domain protein 4
KeywordsHYDROLASE / HhH DNA glycosylase superfamily
Function / homology
Function and homology information


satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol ...satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol / nuclear speck / DNA repair / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Methyl-CpG-binding domain protein 4 / Methyl-CpG binding protein MeCP2/MBD4 / Hypothetical protein; domain 2 / Endonuclease III; domain 1 / DNA glycosylase / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily ...Methyl-CpG-binding domain protein 4 / Methyl-CpG binding protein MeCP2/MBD4 / Hypothetical protein; domain 2 / Endonuclease III; domain 1 / DNA glycosylase / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMorera, S. / Vigouroux, A.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA.
Authors: Morera, S. / Grin, I. / Vigouroux, A. / Couve, S. / Henriot, V. / Saparbaev, M. / Ishchenko, A.A.
History
DepositionMar 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-CpG-binding domain protein 4


Theoretical massNumber of molelcules
Total (without water)19,4161
Polymers19,4161
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.970, 80.970, 74.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Methyl-CpG-binding domain protein 4 / Methyl-CpG-binding endonuclease 1 / Methyl-CpG-binding protein MBD4 / Mismatch-specific DNA N-glycosylase


Mass: 19416.393 Da / Num. of mol.: 1 / Fragment: glycosylase domain of MBD4 (residues 426-580)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Plasmid: pet29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 100 mM Tris-HCl and 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2011
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→40.49 Å / Num. all: 14328 / Num. obs: 13475 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.25 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1661 / % possible all: 72

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IHO

3iho


Resolution: 1.9→40.49 Å / Cor.coef. Fo:Fc: 0.9256 / Cor.coef. Fo:Fc free: 0.8986 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 674 5 %RANDOM
Rwork0.1928 ---
obs0.194 13467 93.81 %-
all-14328 --
Displacement parametersBiso mean: 35.58 Å2
Baniso -1Baniso -2Baniso -3
1--7.0873 Å20 Å20 Å2
2---7.0873 Å20 Å2
3---14.1745 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 0 75 1272
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011240HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.931686HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d420SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes172HARMONIC5
X-RAY DIFFRACTIONt_it1240HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion17.83
X-RAY DIFFRACTIONt_chiral_improper_torsion149SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1472SEMIHARMONIC4
LS refinement shellResolution: 1.9→2.05 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2433 108 4.99 %
Rwork0.2468 2056 -
all0.2466 2164 -
obs--93.81 %

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