8AWP | pdb_00008awp

Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/C106Q)

PDB DOI: https://doi.org/10.2210/pdb8AWP/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: 1.59 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 26.33 kDa
Atom Count: 1,938
Modeled Residue Count: 215
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin_2 domain-containing protein	A, B	114	Thermotoga maritima	Mutation(s): 5 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1H0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.208 (Depositor), 0.208 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.71	α = 90
b = 53.258	β = 90
c = 89.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

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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

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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.