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- PDB-4dk9: Crystal Structure of MBD4 Catalytic Domain Bound to Abasic DNA -

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Basic information

Entry
Database: PDB / ID: 4dk9
TitleCrystal Structure of MBD4 Catalytic Domain Bound to Abasic DNA
Components
  • 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'
  • 5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'
  • Methyl-CpG-binding domain protein 4
KeywordsHYDROLASE/DNA / protein-DNA complex / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.76 Å
AuthorsManvilla, B.A. / Toth, E.A. / Drohat, A.C.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of Human Methyl-Binding Domain IV Glycosylase Bound to Abasic DNA.
Authors: Manvilla, B.A. / Maiti, A. / Begley, M.C. / Toth, E.A. / Drohat, A.C.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
B: 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'
C: 5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'
A: Methyl-CpG-binding domain protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3094
Polymers25,2703
Non-polymers391
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-13 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.999, 55.161, 122.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'


Mass: 3407.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Complementary DNA strand
#2: DNA chain 5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'


Mass: 3191.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Abasic DNA strand
#3: Protein Methyl-CpG-binding domain protein 4 / / Methyl-CpG-binding endonuclease 1 / Methyl-CpG-binding protein MBD4 / Mismatch-specific DNA N-glycosylase


Mass: 18671.521 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (UNP residues 426-580)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2M potassium acetate, 20% PEG 3350, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.75→150 Å / Num. obs: 7618 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.156 / Χ2: 0.985 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.859.70.9417250.8021100
2.85-2.969.80.7297400.8581100
2.96-3.1100.5217480.9931100
3.1-3.26100.3537541.0681100
3.26-3.46100.2417441.1481100
3.46-3.73100.1777560.9511100
3.73-4.11100.1497640.9221100
4.11-4.79.90.117591.0641100
4.7-5.929.80.0977841.0721100
5.92-15090.0818440.952198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→61.1 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.007 / SU ML: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 350 4.6 %RANDOM
Rwork0.2338 ---
obs-7583 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 239.53 Å2 / Biso mean: 105.3622 Å2 / Biso min: 45 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20 Å2
2--2.81 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.76→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 437 1 1 1601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211694
X-RAY DIFFRACTIONr_angle_refined_deg1.8242.2622398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4695139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69923.7556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.04815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.732155
X-RAY DIFFRACTIONr_chiral_restr0.1140.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211148
X-RAY DIFFRACTIONr_mcbond_it4.2381.5703
X-RAY DIFFRACTIONr_mcangle_it6.11421141
X-RAY DIFFRACTIONr_scbond_it2.6833991
X-RAY DIFFRACTIONr_scangle_it4.4564.51257
LS refinement shellResolution: 2.757→2.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 22 -
Rwork0.362 494 -
all-516 -
obs--98.85 %
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)
11.84930.2577-0.430.362-0.06631.5430.17870.076-0.0779-0.0555-0.1320.0684-0.0780.1054-0.04670.24980.024-0.00980.2952-0.01260.2745-10.562913.156-15.8617
20.9142-1.52381.54352.5311-2.09491.1892-0.20550.2171-0.12250.33690.20480.1188-0.60660.01360.00080.3964-0.0527-0.11640.29060.11090.0708-13.645432.0644-21.9874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A438 - 576
2X-RAY DIFFRACTION2B1 - 11
3X-RAY DIFFRACTION2C12 - 22

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