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- PDB-1ngn: Mismatch repair in methylated DNA. Structure of the mismatch-spec... -

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Basic information

Entry
Database: PDB / ID: 1ngn
TitleMismatch repair in methylated DNA. Structure of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4
Componentsmethyl-CpG binding protein MBD4
KeywordsDNA BINDING PROTEIN / mismacth repair in methylated DNA
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 / DNA repair / DNA damage response / chromatin ...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 / DNA repair / DNA damage response / chromatin / DNA binding / nucleus / cytoplasm
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWu, P. / Qiu, C. / Sohail, A. / Zhang, X. / Bhagwat, A.S. / Cheng, X.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4
Authors: Wu, P. / Qiu, C. / Sohail, A. / Zhang, X. / Bhagwat, A.S. / Cheng, X.
History
DepositionDec 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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 protein MBD4


Theoretical massNumber of molelcules
Total (without water)18,5671
Polymers18,5671
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.580, 48.580, 146.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein methyl-CpG binding protein MBD4


Mass: 18567.395 Da / Num. of mol.: 1 / Fragment: glycosylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mbd4 / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2D7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.26
Details: PEG 2000 monomethyl ether, ammonium sulfate, ethylene glycol, sodium citrate, pH 5.26, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122-27 %PEG2000 MME1reservoir
2190-230 mMammonium sulfate1reservoir
310-15 %ethylene glycol1reservoir
4100 mMsodium citrate1reservoirpH5.26

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONNSLS X12C20.9789, 0.97865, 0.95
SYNCHROTRONNSLS X26C31.1
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEOct 16, 2000
BRANDEIS - B22CCDNov 5, 2000
ADSC QUANTUM 43CCDFeb 8, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic mirrorSINGLE WAVELENGTHMx-ray1
2NSLS X12C opticsMADMx-ray1
3NSLS X26C opticsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97891
30.978651
40.951
51.11
ReflectionResolution: 2.1→20 Å / Num. all: 12345 / Num. obs: 12345 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.73 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 42.7
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.098 / Num. unique all: 585 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 107778
Reflection shell
*PLUS
% possible obs: 99.8 % / Num. unique obs: 585

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.33 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: proXPLOR:tein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.263 894 -RANDOM
Rwork0.213 ---
all-11028 --
obs-11028 99.5 %-
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å21.87 Å20 Å2
2--2.09 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-19.33 Å
Luzzati sigma a0.19 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 0 92 1306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.4
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_improper_angle_d0.65
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.1-2.180.28717880.2850.0211234594.1
2.18180212580.8
Refinement
*PLUS
Highest resolution: 2.1 Å / Num. reflection obs: 21552 / % reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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