8A9F | pdb_00008a9f

Thaumatin, 9-11 fs FEL pulses as determined by XTCAV

PDB DOI: https://doi.org/10.2210/pdb8A9F/pdb

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

Deposited: 2022-06-28 Released: 2023-07-12
Deposition Author(s): Barends, T., Nass, K., Gorel, A., Schlichting, I.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.204 (Depositor), 0.214 (DCC)
R-Value Work:
0.173 (Depositor), 0.182 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8A9F

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

Literature

Microcrystallization paper

Gorel, A., Nass, K., Barends, T., Schlichting, I.

To be published.

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,700
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-1	A [auth AAA]	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 AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.204 (Depositor), 0.214 (DCC)
R-Value Work: 0.173 (Depositor), 0.182 (DCC)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.25	α = 90
b = 58.25	β = 90
c = 150.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-12

Deposition Author(s):

Schlichting, I.

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-07-12
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.