1LXZ

Structure of thaumatin crystallized in the presence of glycerol

PDB DOI: https://doi.org/10.2210/pdb1LXZ/pdb

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

Deposited: 2002-06-06 Released: 2003-01-14
Deposition Author(s): Charron, C., Kadri, A., Robert, M.C., Giege, R., Lorber, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.195
R-Value Work: 0.178
R-Value Observed: 0.179

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin.

Charron, C., Kadri, A., Robert, M.C., Giege, R., Lorber, B.

(2002) Acta Crystallogr D Biol Crystallogr 58: 2060-2065

PubMed: 12454465 Search on PubMed
DOI: https://doi.org/10.1107/s0907444902017183
Primary Citation of Related Structures:
1LXZ, 1LY0

PubMed Abstract:
The intensely sweet protein thaumatin has been crystallized at 293 K in the presence of sodium tartrate and 25%(v/v) glycerol for X-ray diffraction data collection at 100 K. A comparison of the three-dimensional structure model derived from a crystal grown in the presence of glycerol with that of a control deprived of this additive reveals only minor changes in the overall structure but a approximately 20% reduction in the number of water molecules. X-ray topography analyses show that the overall quality of the crystals prepared in the presence of this cryoprotectant is enhanced.

Organizational Affiliation

Département 'Mécanismes et Macromolécules de la Synthèse Protéique et Cristallogenèse' UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15Rue René Descartes, F-67084 Strasbourg Cedex, France.

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,821
Modelled Residue Count: 207
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% 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: 1.25 Å
R-Value Free: 0.195
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.801	α = 90
b = 57.801	β = 90
c = 149.96	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-01-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-01-14
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary