8TM8 | pdb_00008tm8

Monomer structure of monellin loop1 mutant (YENKG)

PDB DOI: https://doi.org/10.2210/pdb8TM8/pdb

Classification: PLANT PROTEIN
Organism(s): Dioscoreophyllum cumminsii
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-07-28 Released: 2024-12-18
Deposition Author(s): Manjula, R., Pavithra, G.C., Ramaswamy, S., Gosavi, S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.261 (Depositor), 0.262 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Monomer structure of monellin loop1 mutant (YENKG)

Pavithra, G.C., Manjula, R., Ramaswamy, S., Gosavi, S.

To be published.

Macromolecule Content

Total Structure Weight: 21.42 kDa
Atom Count: 1,500
Modeled Residue Count: 176
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monellin chain B,Monellin chain A	A, B	91	Dioscoreophyllum cumminsii	Mutation(s): 0
UniProt
Find proteins for P02881 (Dioscoreophyllum cumminsii) Explore P02881 Go to UniProtKB: P02881
Find proteins for P02882 (Dioscoreophyllum cumminsii) Explore P02882 Go to UniProtKB: P02882
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P02881P02882
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.261 (Depositor), 0.262 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.139	α = 90
b = 58.789	β = 91.91
c = 45.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release

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.