7RIJ | pdb_00007rij

[I11G]hyen D

PDB DOI: https://doi.org/10.2210/pdb7RIJ/pdb

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

Deposited: 2021-07-20 Released: 2021-09-22
Deposition Author(s): Du, Q., Huang, Y.H., Wang, C.K., Craik, D.J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.162 (Depositor), 0.160 (DCC)
R-Value Work:
0.146 (Depositor), 0.150 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 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: 6.48 kDa
Atom Count: 509
Modeled Residue Count: 60
Deposited Residue Count: 60
Unique protein chains: 2

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-[I11L]hyen D	B	30	Pigea enneasperma	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.162 (Depositor), 0.160 (DCC)
R-Value Work: 0.146 (Depositor), 0.150 (DCC)
R-Value Observed: 0.148 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.655	α = 65.58
b = 23.85	β = 66.17
c = 24.246	γ = 76.03

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: 2021-09-22

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release
Version 1.1: 2021-09-29
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-11-13
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.