7O5J | pdb_00007o5j

Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and pinkIndexer

PDB DOI: https://doi.org/10.2210/pdb7O5J/pdb

Classification: PLANT PROTEIN
Organism(s): Thaumatococcus daniellii
Expression System: Thaumatococcus daniellii
Mutation(s): No

Deposited: 2021-04-08 Released: 2022-04-20
Deposition Author(s): Nass, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.174 (Depositor), 0.180 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and pinkIndexer

Nass, K.

To be published.

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,632
Modeled Residue Count: 207
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin-1	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883 Go to UniProtKB: P02883
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA 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]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.174 (Depositor), 0.180 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data: https://doi.org/10.11577/1814882

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.52	α = 90
b = 58.52	β = 90
c = 151.3	γ = 90

Software Package:

Software Name	Purpose
CrystFEL	data collection
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2023-12-13
Changes: Data collection, Database references
Version 1.2: 2024-10-23
Changes: Structure summary

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.