8AWN | pdb_00008awn

Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant C106Q

PDB DOI: https://doi.org/10.2210/pdb8AWN/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: 1.45 Å
R-Value Free:
0.173 (Depositor), 0.170 (DCC)
R-Value Work:
0.142 (Depositor), 0.140 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
View more details

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: 13.19 kDa
Atom Count: 1,106
Modeled Residue Count: 110
Deposited Residue Count: 114
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin_2 domain-containing protein	A	114	Thermotoga maritima	Mutation(s): 1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.173 (Depositor), 0.170 (DCC)
R-Value Work: 0.142 (Depositor), 0.140 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.266	α = 90
b = 53.266	β = 90
c = 115.326	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.