6RVO | pdb_00006rvo

Multicrystal dataset of thaumatin collected using a multilayer monochromator.

PDB DOI: https://doi.org/10.2210/pdb6RVO/pdb

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

Deposited: 2019-05-31 Released: 2019-06-19
Deposition Author(s): Sandy, J., Sanchez-Weatherby, J., Mikolajek, H., Winter, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.176 (Depositor), 0.176 (DCC)
R-Value Work:
0.142 (Depositor), 0.142 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RVO

This is version 1.4 of the entry. See complete history.

Literature

Protein-to-structure pipeline for ambient-temperature crystallography at VMXi

Mikolajek, H., Sanchez-Weatherby, J., Sandy, J., Gildea, R.G., Campeotto, I., Cheruvara, H., Clarke, J.D., Foster, T., Fujii, S., Paulsen, I.T., Shah, B.S., Hough, M.A.

(2023) IUCrJ

DOI: https://doi.org/10.1107/S2052252523003810

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,704
Modeled Residue Count: 206
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: 1.97 Å
R-Value Free: 0.176 (Depositor), 0.176 (DCC)
R-Value Work: 0.142 (Depositor), 0.142 (DCC)
R-Value Observed: 0.145 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.563	α = 90
b = 58.563	β = 90
c = 151.496	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Sanchez-Weatherby, J.

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2019-08-21
Changes: Data collection
Version 1.2: 2023-05-17
Changes: Database references, Refinement description
Version 1.3: 2024-02-07
Changes: Data collection, Refinement description
Version 1.4: 2024-10-23
Changes: 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.