8AWO | pdb_00008awo

Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant AIFQ (Y7A/M38I/Y83F/C106Q)

PDB DOI: https://doi.org/10.2210/pdb8AWO/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-08-30 Released: 2023-03-08
Deposition Author(s): Grininger, C., Steiner, K., Gruber, K., Pavkov-Keller, T.
Funding Organization(s): Austrian Research Promotion Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Engineering TM1459 for Stabilisation against Inactivation by Amino Acid Oxidation

Grill, B., Pavkov-Keller, T., Grininger, C., Darnhofer, B., Gruber, K., Hall, M., Schwab, H., Steiner, K.

(2023) Chem Ing Tech

DOI: https://doi.org/10.1002/cite.202200176

Macromolecule Content

Total Structure Weight: 26.06 kDa
Atom Count: 1,989
Modeled Residue Count: 218
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin_2 domain-containing protein	A, B	114	Thermotoga maritima	Mutation(s): 4 Gene Names: TM_1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H0 Go to UniProtKB: Q9X1H0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1H0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.795	α = 90
b = 53.733	β = 90
c = 90.435	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Pavkov-Keller, T.

Funding Organization	Location	Grant Number
Austrian Research Promotion Agency	Austria	--

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Database references, Refinement description

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.