1L9G | pdb_00001l9g

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 (Depositor)
R-Value Work:
0.226 (Depositor)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1L9G

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
Modeled Residue Count: 191
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical protein	A	192	Thermotoga maritima	Mutation(s): 0 Gene Names: TMUNG EC: 3.2.2.27
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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] mmCIF 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 (Depositor)
R-Value Work: 0.226 (Depositor)
R-Value Observed: 0.231 (Depositor)

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

View more in-depth experimental data

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

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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.