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- PDB-3vxx: Crystal structure of methyl CpG binding domain of MBD4 in complex... -

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Basic information

Entry
Database: PDB / ID: 3vxx
TitleCrystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence
Components
  • DNA (5'-D(*GP*TP*CP*(5CM)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
  • DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / methyl CpG binding domain / protein-DNA complex / versatile base recognition / HYDROLASE-DNA complex
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / : / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear speck / DNA repair ...Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / : / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear speck / DNA repair / DNA damage response / chromatin / DNA binding / nucleus / cytoplasm
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
ACETATE ION / DNA / DNA (> 10) / Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsOtani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Ariyoshi, M. / Shirakawa, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4
Authors: Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Kimura, H. / Suetake, I. / Tajima, S. / Ariyoshi, M. / Shirakawa, M.
History
DepositionSep 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 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 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')
C: DNA (5'-D(*GP*TP*CP*(5CM)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,95912
Polymers16,4193
Non-polymers5409
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-4 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.182, 93.829, 55.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-207-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 7829.089 Da / Num. of mol.: 1 / Fragment: methyl CpG binding domain, UNP residues 69-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mbd4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z2D7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')


Mass: 4263.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis
#3: DNA chain DNA (5'-D(*GP*TP*CP*(5CM)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')


Mass: 4325.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis

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Non-polymers , 3 types, 132 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 7% PEG 10000, 0.1M sodium acetate, 0.2M sodium chloride, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 12096 / Num. obs: 12048 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 41.31 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VXV

3vxv


Resolution: 2.204→28.339 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 574 4.77 %
Rwork0.1955 --
obs0.1965 12027 99.54 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.734 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 78.83 Å2 / Biso min: 20.15 Å2
Baniso -1Baniso -2Baniso -3
1--13.1184 Å20 Å20 Å2
2--11.4286 Å2-0 Å2
3---1.6898 Å2
Refinement stepCycle: LAST / Resolution: 2.204→28.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 570 36 123 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061201
X-RAY DIFFRACTIONf_angle_d1.1931727
X-RAY DIFFRACTIONf_dihedral_angle_d23.213471
X-RAY DIFFRACTIONf_chiral_restr0.062183
X-RAY DIFFRACTIONf_plane_restr0.006126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.204-2.42570.34091420.272128302972100
2.4257-2.77640.33331410.260128282969100
2.7764-3.4970.20731330.191328582991100
3.497-28.34140.17381580.16842937309599
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)
10.1975-0.28880.23690.6312-0.03990.7690.00930.14660.0347-0.1660.046-0.0066-0.05160.0524-0.03260.2086-0.0364-0.00340.21840.00660.18763.49612.09714.4118
22.34681.49760.15161.18460.34440.2642-0.1097-0.3115-0.3255-0.2639-0.0099-0.2258-0.1719-0.10870.05120.2592-0.0793-0.01210.28310.10620.302318.935311.789-13.9496
31.2729-0.32610.42590.581-0.52760.4689-0.2826-0.08080.1478-0.23690.1178-0.13580.067-0.00540.1290.2233-0.05660.01950.383-0.0170.256822.756813.1583-11.3946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and (resseq 72:134))A72 - 134
2X-RAY DIFFRACTION2(chain 'B' and (resseq 1:14))B1 - 14
3X-RAY DIFFRACTION3(chain 'C' and (resseq 1:14))C1 - 14

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