8RS3 | pdb_00008rs3

Thaumatin measured via serial crystallography from a kapton HARE-chip (50 micron)

PDB DOI: https://doi.org/10.2210/pdb8RS3/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Thaumatococcus daniellii
Mutation(s): No

Deposited: 2024-01-24 Released: 2025-02-05
Deposition Author(s): Bosman, R., Prester, A., von Soosten, L., Dibenedetto, S., Bartels, K., Sung, S., von Stetten, D., Mehrabi, P., Schulz, E.C.
Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Economic Affairs and Energy

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8RS3

This is version 1.0 of the entry. See complete history.

Literature

Kapton-based HARE chips for fixed-target serial crystallography

Bosman, R., Prester, A., von Soosten, L., Dibenedetto, S., Bartels, K., Sung, S., von Stetten, D., Mehrabi, P., Blatter, G., Lu, G., Bernhard, S., Osbild, M., Schulz, E.C.

To be published.

Macromolecule Content

Total Structure Weight: 25.63 kDa
Atom Count: 1,709
Modeled Residue Count: 206
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	A [auth X]	235	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883 Go to UniProtKB: P02883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.183 (Depositor), 0.184 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.2	α = 90
b = 58.2	β = 90
c = 150.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-05

Deposition Author(s):

von Soosten, L.

Dibenedetto, S.

von Stetten, D.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	458246365
German Research Foundation (DFG)	Germany	451079909
German Federal Ministry for Economic Affairs and Energy	Germany	01KI2114

Revision History (Full details and data files)

Version 1.0: 2025-02-05
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.