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- PDB-3vxv: Crystal structure of methyl CpG Binding Domain of MBD4 in complex... -

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Basic information

Entry
Database: PDB / ID: 3vxv
TitleCrystal structure of methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence
Components
  • DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-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 / SAD / Resolution: 2 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

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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*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,96912
Polymers16,4203
Non-polymers5509
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-8 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.074, 94.989, 54.738
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
11A-320-

HOH

21B-201-

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
#3: DNA chain DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')


Mass: 4326.812 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 163 molecules

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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.5365.11
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop4.4pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop4.4pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2952
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory AR-NE3A2
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDJan 27, 2010
ADSC QUANTUM 2702CCDOct 14, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 2→50 Å / Num. all: 16110 / Num. obs: 16062 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 36.36 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→23.747 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 801 5.01 %
Rwork0.1875 --
obs0.1892 16002 99.44 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.253 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 84.75 Å2 / Biso mean: 40.4743 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1--12.9528 Å20 Å20 Å2
2--10.7675 Å2-0 Å2
3---2.1853 Å2
Refinement stepCycle: LAST / Resolution: 2→23.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms525 570 36 154 1285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181205
X-RAY DIFFRACTIONf_angle_d2.0711728
X-RAY DIFFRACTIONf_dihedral_angle_d23.326479
X-RAY DIFFRACTIONf_chiral_restr0.119185
X-RAY DIFFRACTIONf_plane_restr0.01123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9989-2.1240.27071500.233224752625100
2.124-2.28790.36771390.25532493263299
2.2879-2.51790.29241480.233825002648100
2.5179-2.88170.27131250.217825452670100
2.8817-3.62860.22351170.171125662683100
3.6286-23.74890.16331220.16262622274498
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)
10.6284-0.43140.32560.9797-0.62421.5410.0083-0.01410.0059-0.09710.0234-0.07290.0997-0.0137-0.04870.2326-0.00730.00260.2517-0.02450.2424-3.3944-11.81314.375
21.77491.6014-0.46282.1899-1.0130.5161-0.0418-0.27280.2781-0.2738-0.05460.36790.11460.22620.03830.3457-0.0759-0.02260.3937-0.11410.355-18.9331-12.0063-13.7962
33.78030.29870.03730.62640.35340.3422-0.2650.0063-0.3741-0.18410.11250.14630.0021-0.11570.1730.3022-0.0426-0.00950.4634-0.00210.3583-22.6605-13.3668-11.2981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA71 - 135
2X-RAY DIFFRACTION2chain BB1 - 14
3X-RAY DIFFRACTION3chain CC1 - 14

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