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- PDB-5chz: Structure of wild-type human MBD4 bound to a G:T mismatch -

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Basic information

Entry
Database: PDB / ID: 5chz
TitleStructure of wild-type human MBD4 bound to a G:T mismatch
Components
  • 12-mer DNA(G)
  • 5-mer DNA
  • 7-mer DNA
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / hMBD4 / DNA glycosylase / G:T mismatch / 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 MeCP2/MBD4 / Hypothetical protein; domain 2 / DNA glycosylase / Endonuclease III; domain 1 / 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 / DNA glycosylase / Endonuclease III; domain 1 / 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
DNA / DNA (> 10) / Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsOuzon-Shubeita, H. / Lin, Y.-L. / Lee, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R21ES023101 United States
Welch FoundationF-1741 United States
CitationJournal: To Be Published
Title: Structure of wild-type human MBD4 bound to a G:T mismatch
Authors: Ouzon-Shubeita, H. / Lin, Y.-L. / Lee, S.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
C: 7-mer DNA
D: 12-mer DNA(G)
B: 5-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8115
Polymers29,7874
Non-polymers241
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-31 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.886, 54.875, 104.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 endonuclease 1 / Methyl-CpG-binding protein MBD4 / Mismatch-specific DNA N-glycosylase


Mass: 22487.832 Da / Num. of mol.: 1 / Fragment: UNP residues 426-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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DNA chain , 3 types, 3 molecules CDB

#2: DNA chain 7-mer DNA


Mass: 2098.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 12-mer DNA(G)


Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 5-mer DNA


Mass: 1505.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 157 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.01 Å3/Da / Density % sol: 36.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 21% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.83→38.91 Å / Num. obs: 20686 / % possible obs: 97.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 30.7
Reflection shellResolution: 1.83→1.895 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.15 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OFA

4ofa


Resolution: 1.83→38.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.48 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20899 1067 5.1 %RANDOM
Rwork0.17369 ---
obs0.17546 19653 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0 Å2
2--0.09 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 488 1 156 1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0171783
X-RAY DIFFRACTIONr_bond_other_d0.0010.021434
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.7072519
X-RAY DIFFRACTIONr_angle_other_deg1.05533322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24223.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57315213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.644156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211643
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.052.094559
X-RAY DIFFRACTIONr_mcbond_other2.0222.087558
X-RAY DIFFRACTIONr_mcangle_it2.8043.121697
X-RAY DIFFRACTIONr_mcangle_other2.8023.129698
X-RAY DIFFRACTIONr_scbond_it3.7242.8771224
X-RAY DIFFRACTIONr_scbond_other3.7252.8771223
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2884.2331822
X-RAY DIFFRACTIONr_long_range_B_refined6.98222.8622362
X-RAY DIFFRACTIONr_long_range_B_other6.98122.8672363
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.829→1.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 79 -
Rwork0.203 1271 -
obs--85.61 %

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