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- PDB-7ray: Crystal structure of MBD2 with DNA -

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Basic information

Entry
Database: PDB / ID: 7ray
TitleCrystal structure of MBD2 with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
  • Methyl-CpG-binding domain protein 2
KeywordsDNA BINDING PROTEIN/DNA / DNA binding protein-DNA complex / MBD / TAM / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / siRNA binding / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway ...satellite DNA binding / ventricular cardiac muscle tissue development / NuRD complex / maternal behavior / siRNA binding / C2H2 zinc finger domain binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / cellular response to organic cyclic compound / positive regulation of Wnt signaling pathway / embryonic organ development / heterochromatin / response to mechanical stimulus / RNA Polymerase I Promoter Opening / response to nutrient levels / NoRC negatively regulates rRNA expression / Wnt signaling pathway / response to estradiol / regulation of cell population proliferation / protein-containing complex assembly / molecular adaptor activity / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Methyl-CpG binding protein 2/3, C-terminal domain / Methyl-CpG-binding domain protein 2/3, p55-binding region / C-terminal domain of methyl-CpG binding protein 2 and 3 / p55-binding region of Methyl-CpG-binding domain proteins MBD / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Methyl-CpG-binding domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLiu, K. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of MBD2 with DNA
Authors: Liu, K. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionJul 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-CpG-binding domain protein 2
B: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,1605
Polymers16,1603
Non-polymers02
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-3 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.599, 71.992, 126.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Methyl-CpG-binding domain protein 2 / Demethylase / DMTase / Methyl-CpG-binding protein MBD2


Mass: 8805.196 Da / Num. of mol.: 1 / Fragment: UNP residues 143-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UBB5
#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')


Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M disodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.78→42.04 Å / Num. obs: 33442 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 28.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.827.30.47149380.9710.1850.50698.5
9.08-42.045.60.0321550.9980.0150.03698.9

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Processing

Software
NameVersionClassification
PHENIXdev_1439refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C2Z

6c2z


Resolution: 1.78→36 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.43 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 1587 5.05 %
Rwork0.2092 29843 -
obs0.2113 31430 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.66 Å2 / Biso mean: 34.74 Å2 / Biso min: 16.85 Å2
Refinement stepCycle: final / Resolution: 1.78→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms557 488 2 72 1119
Biso mean--35.65 34.58 -
Num. residues----98
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071140
X-RAY DIFFRACTIONf_angle_d1.2171645
X-RAY DIFFRACTIONf_chiral_restr0.051173
X-RAY DIFFRACTIONf_plane_restr0.008131
X-RAY DIFFRACTIONf_dihedral_angle_d27.22459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7801-1.83750.32071600.3001270898
1.8375-1.90320.34431640.305264898
1.9032-1.97940.31771760.2737267299
1.9794-2.06950.33571240.2641273499
2.0695-2.17860.29271550.2638267499
2.1786-2.3150.34431450.25352730100
2.315-2.49370.2591190.2415276299
2.4937-2.74460.28581470.25362725100
2.7446-3.14160.24071260.2297274899
3.1416-3.95730.2341330.1859269899
3.9573-35.9960.1831380.1432744100
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)
14.2328-0.7239-0.07950.5108-0.84021.8566-0.3644-0.6817-0.0560.18080.2657-0.1522-0.2598-0.1150.03070.25060.1169-0.01660.29440.00950.154-27.91319.376710.5959
20.0170.18870.89220.97590.46031.0392-0.1593-0.0875-0.10430.28930.01560.14810.2203-0.0837-0.00030.27490.0480.07280.22940.05190.3001-41.370614.043917.9895
31.0537-1.20360.7841.17740.98020.5201-0.1474-0.0265-0.16670.50150.02610.3246-0.0537-0.0901-0.01290.24580.08230.08690.24480.02520.2589-41.704714.105416.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA142 - 215
2X-RAY DIFFRACTION2chain BB1 - 12
3X-RAY DIFFRACTION3chain CC1 - 12

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