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- PDB-3iho: The C-terminal glycosylase domain of human MBD4 -

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Basic information

Entry
Database: PDB / ID: 3iho
TitleThe C-terminal glycosylase domain of human MBD4
ComponentsMethyl-CpG-binding domain protein 4
KeywordsHYDROLASE / MBD4 / Structural Genomics / Structural Genomics Consortium / SGC / DNA damage / DNA repair / DNA-binding / Nucleus
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
Methyl-CpG-binding domain protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsAmaya, M.F. / Xu, C. / Bian, C.B. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The C-terminal glycosylase domain of human MBD4
Authors: Xu, C. / Bian, C.B. / Amaya, M.F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)16,6121
Polymers16,6121
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.541, 83.541, 73.956
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 protein MBD4 / Methyl-CpG-binding endonuclease 1 / Mismatch-specific DNA N-glycosylase


Mass: 16612.084 Da / Num. of mol.: 1 / Fragment: C-terminal glycosylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M Li Sulfate, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.697→51.71 Å / Num. obs: 5287 / % possible obs: 93.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.697-2.82.60.315164.3
2.8-2.912.90.322179.3
2.91-3.043.10.304194.2
3.04-3.23.60.216199
3.2-3.43.90.169199.9
3.4-3.6640.1351100
3.66-4.034.10.1191100
4.03-4.624.10.0841100
4.62-5.8140.0681100
5.81-404.20.039199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→51.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.469 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29003 218 4.5 %RANDOM
Rwork0.18248 ---
obs0.18735 4589 90.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.405 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.94 Å20 Å2
2--1.89 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.7→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 0 12 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9231626
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27123.50957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87715183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.907155
X-RAY DIFFRACTIONr_chiral_restr0.1250.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021923
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8041.5693
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6121119
X-RAY DIFFRACTIONr_scbond_it2.5443496
X-RAY DIFFRACTIONr_scangle_it4.2284.5507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 11 -
Rwork0.164 207 -
obs--57.22 %
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)
12.3869-1.2729-0.57520.90380.270.1996-0.1071-0.25260.24840.21380.1043-0.2419-0.04050.0850.00280.2552-0.0088-0.02560.22420.00270.238429.6082-2.298418.8875
21.90791.5615-1.80562.2423-0.49973.3853-0.0240.14310.010.06910.10430.04920.0285-0.1239-0.08020.09590.021-0.00960.1004-0.02950.032218.5195-16.739819.052
31.36562.14411.95214.50490.88537.1687-0.6490.3560.2393-0.48160.32270.3758-1.82030.79920.32630.6046-0.2387-0.11730.25380.05660.04427.5193-1.4038.0913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A411 - 422
2X-RAY DIFFRACTION2A423 - 528
3X-RAY DIFFRACTION3A529 - 548

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