7RII | pdb_00007rii

[I11L]hyen D crystal structure

PDB DOI: https://doi.org/10.2210/pdb7RII/pdb

Classification: PLANT PROTEIN
Organism(s): Pigea enneasperma
Mutation(s): Yes

Deposited: 2021-07-20 Released: 2021-09-29
Deposition Author(s): Du, Q., Huang, Y.H., Craik, D.J., Wang, C.K.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.205 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Enabling efficient folding and high-resolution crystallographic analysis of bracelet cyclotides

Craik, D.J., Huang, Y.H., Wang, C.K., Du, Q., King, G.

(2021) Molecules 26(18): 5554

DOI: https://doi.org/10.3390/molecules26185554

Macromolecule Content

Total Structure Weight: 3.28 kDa
Atom Count: 260
Modeled Residue Count: 30
Deposited Residue Count: 30
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclotide hyen-D	A	30	Pigea enneasperma	Mutation(s): 1
UniProt
Find proteins for C0HLN8 (Pigea enneasperma) Explore C0HLN8 Go to UniProtKB: C0HLN8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0HLN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.205 (Depositor), 0.200 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.755	α = 87.25
b = 21.153	β = 82.94
c = 26.296	γ = 89.13

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE200100012

Revision History (Full details and data files)

Version 1.0: 2021-09-29
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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.