1L9G

CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM T. MARITIMA

PDB DOI: https://doi.org/10.2210/pdb1L9G/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-03-22 Released: 2003-05-27
Deposition Author(s): Rajashankar, K.R., Dodatko, T., Thirumuruhan, R.A., Sandigursky, M., Bresnik, A., Chance, M.R., Franklin, W.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.281
R-Value Work: 0.226
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of uracil-DNA glycosylase from T. Maritima

Rajashankar, K.R., Dodatko, T., Thirumuruhan, R.A., Sandigursky, M., Bresnik, A., Chance, M.R., Franklin, W.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 21.98 kDa
Atom Count: 1,575
Modelled Residue Count: 191
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical protein	A	192	Thermotoga maritima	Mutation(s): 0 Gene Names: TMUNG
UniProt
Find proteins for Q9WYY1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYY1 Go to UniProtKB: Q9WYY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.281
R-Value Work: 0.226
R-Value Observed: 0.231
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.5	α = 90
b = 60.5	β = 90
c = 127.4	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-05-27

Deposition Author(s):

Rajashankar, K.R.

Thirumuruhan, R.A.

Sandigursky, M.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2003-05-27
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-02-03
Changes: Derived calculations, Structure summary
Version 1.5: 2024-02-14
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.