4OFA | pdb_00004ofa

Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis

PDB DOI: https://doi.org/10.2210/pdb4OFA/pdb
NAKB: 4OFA

Classification: HYDROLASE/DNA
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2014-01-14 Released: 2015-04-22
Deposition Author(s): Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.182 (Depositor), 0.192 (DCC)
R-Value Work:
0.134 (Depositor), 0.148 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structure of MBD4 bound to G:T mispair DNA

Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.

To be published.

Macromolecule Content

Total Structure Weight: 29.85 kDa
Atom Count: 1,919
Modeled Residue Count: 166
Deposited Residue Count: 216
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 4	A	192	Homo sapiens	Mutation(s): 1 Gene Names: MBD4, MED1 EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O95243 (Homo sapiens) Explore O95243 Go to UniProtKB: O95243
PHAROS: O95243 GTEx: ENSG00000129071
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95243
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
12-mer DNA(T)	B [auth C]	12	N/A
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Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
12-mer DNA(G)	C [auth D]	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.182 (Depositor), 0.192 (DCC)
R-Value Work: 0.134 (Depositor), 0.148 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.561	α = 90
b = 55.534	β = 90
c = 104.212	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Ouzon-Shubeita, H.

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.