8DWF | pdb_00008dwf

Glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with substrate adenine

PDB DOI: https://doi.org/10.2210/pdb8DWF/pdb
NAKB: 8DWF

Classification: HYDROLASE/DNA
Organism(s): Geobacillus stearothermophilus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-08-01 Released: 2023-08-09
Deposition Author(s): Russelburg, L.P., Demir, M., David, S.S., Horvath, M.P.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY

Russelburg, L.P., Demir, M., Cedeno, K., David, S.S., Horvath, M.P.

To be published.

Macromolecule Content

Total Structure Weight: 98.19 kDa
Atom Count: 6,412
Modeled Residue Count: 745
Deposited Residue Count: 774
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine DNA glycosylase	A, D	365	Geobacillus stearothermophilus	Mutation(s): 1 Gene Names: mutY EC: 3.2.2.31
UniProt
Find proteins for P83847 (Geobacillus stearothermophilus) Explore P83847 Go to UniProtKB: P83847
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83847
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(APAPGPAPCP(8OG)PTPGPGPAP*C)-3')	B, E	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(TPGPTPCPCPAPAPGPTPCP*T)-3')	C, F	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain G [auth A] MOL2 format, chain L [auth D] MOL2 format, chain G [auth A] mmCIF format, chain L [auth D] mmCIF format, chain G [auth A]	G [auth A], L [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain K [auth B] MOL2 format, chain P [auth E] MOL2 format, chain K [auth B] mmCIF format, chain P [auth E] mmCIF format, chain K [auth B]	K [auth B], P [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain K [auth B] Focus chain P [auth E] Interactions & Density Focus chain K [auth B] Focus chain P [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth A] MOL2 format, chain O [auth D] MOL2 format, chain J [auth A] mmCIF format, chain O [auth D] mmCIF format, chain J [auth A]	J [auth A], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], M [auth D], N [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.08	α = 90
b = 137.9	β = 101.44
c = 74.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1905304
National Science Foundation (NSF, United States)	United States	1905249
National Science Foundation (NSF, United States)	United States	1610721
National Science Foundation (NSF, United States)	United States	1608934