4XVB | pdb_00004xvb

Recombinant thaumatin in the presence of 1.5M PST at 293K

PDB DOI: https://doi.org/10.2210/pdb4XVB/pdb

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

Deposited: 2015-01-27 Released: 2016-02-03
Deposition Author(s): Masuda, T., Okubo, K., Mikami, B.
Funding Organization(s): The Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.130 (Depositor), 0.130 (DCC)
R-Value Work:
0.109 (Depositor), 0.111 (DCC)
R-Value Observed:
0.110 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4XVB

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

Literature

Structure of the recombinant thaumatin in the presence of PST at room temperature

Masuda, T., Okubo, K., Mikami, B.

To be published.

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,922
Modeled Residue Count: 207
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin I	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% 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 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: 1.52 Å
R-Value Free: 0.130 (Depositor), 0.130 (DCC)
R-Value Work: 0.109 (Depositor), 0.111 (DCC)
R-Value Observed: 0.110 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.487	α = 90
b = 58.487	β = 90
c = 151.609	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data processing
HKL-2000	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

Funding Organization	Location	Grant Number
The Japan Society for the Promotion of Science	Japan	no. 22580105 and no. 25450167

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Derived calculations
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary

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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.