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- PDB-4lg7: Crystal structure MBD4 MBD domain in complex with methylated CpG DNA -

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Basic information

Entry
Database: PDB / ID: 4lg7
TitleCrystal structure MBD4 MBD domain in complex with methylated CpG DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / Structural Genomics Consortium / SGC / HYDROLASE-DNA complex
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 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / 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 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / DNA glycosylase / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsXu, C. / Tempel, W. / Wernimont, A.K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure MBD4 MBD domain in complex with methylated CpG DNA
Authors: Xu, C. / Tempel, W. / Wernimont, A.K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-CpG-binding domain protein 4
B: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)15,18014
Polymers15,1803
Non-polymers011
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-1 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.367, 78.209, 40.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: 7824.997 Da / Num. of mol.: 1 / Fragment: UNP residues 83-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#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 / Details: synthetic
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically

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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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG400, 5% MPD, 0.2 M sodium chloride, 0.1 M HEPES. protein:dna 1:1.2., pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.45→41.746 Å / Num. all: 5780 / Num. obs: 5780 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rsym value: 0.09 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.647.10.9210.957008040.92198.8
2.64-2.870.571.455067820.5799.2
2.8-2.9970.396251077260.39699.6
2.99-3.2370.1654.348146890.16599.6
3.23-3.546.90.14.643866390.198.8
3.54-3.956.70.089.338975800.0899.9
3.95-4.566.50.06211.734435300.062100
4.56-5.596.50.0491428974480.049100
5.59-7.916.30.04115.622853620.04199.9
7.91-36.0045.30.02918.311762200.02999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.12data extraction
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3VXX

3vxx


Resolution: 2.5→36 Å / Cor.coef. Fo:Fc: 0.9332 / Cor.coef. Fo:Fc free: 0.9179 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0
Details: Refmac, phenix, coot, molprobity server were also used during refinement. We note the small number of reflections in the x-validation free set and a significant discrepancy between average ...Details: Refmac, phenix, coot, molprobity server were also used during refinement. We note the small number of reflections in the x-validation free set and a significant discrepancy between average refined and Wilson B-factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 259 4.51 %RANDOM
Rwork0.2122 ---
obs0.2142 5747 99.12 %-
Displacement parametersBiso max: 112.01 Å2 / Biso mean: 57.9513 Å2 / Biso min: 29.74 Å2
Baniso -1Baniso -2Baniso -3
1--18.6227 Å20 Å20 Å2
2--8.8159 Å20 Å2
3---9.8068 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 2.5→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 488 11 0 983
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d459SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes8HARMONIC2
X-RAY DIFFRACTIONt_gen_planes100HARMONIC5
X-RAY DIFFRACTIONt_it1043HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact951SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1043HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1511HARMONIC21.35
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion20.25
LS refinement shellResolution: 2.5→2.79 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3506 73 4.65 %
Rwork0.2613 1498 -
all0.2656 1571 -
obs--99.12 %
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)
13.0521.48810.21569.3351.97135.0540.0805-0.07980.0739-0.0033-0.03820.2924-0.1166-0.092-0.0422-0.106-0.0027-0.0194-0.1517-0.00220.019954.487424.723453.9133
27.20730.73290.71555.0506-0.916111.9182-0.01760.45010.1713-0.44780.31150.04850.25570.4761-0.2939-0.05870.10140.0615-0.08860.0395-0.150358.34968.335251.5271
312.55440.09310.93023.29330.12789.20910.09170.3055-0.0473-0.31130.1339-0.10460.17660.1422-0.22560.08350.08070.0558-0.2683-0.0073-0.14359.59419.27451.2163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A83 - 145
2X-RAY DIFFRACTION2{ B|* }B1 - 12
3X-RAY DIFFRACTION3{ C|* }C1 - 12

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