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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 6.48 kDa 
• Atom Count: 509 
• Modeled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 2

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Non-standard Monomers  13 Unique
ID	Chains	Type	Formula	2D Diagram
DAL	B	D-PEPTIDE LINKING	C3 H7 N O2
DCY	B	D-PEPTIDE LINKING	C3 H7 N O2 S
DGL	B	D-PEPTIDE LINKING	C5 H9 N O4
DIL	B	D-PEPTIDE LINKING	C6 H13 N O2
DLE	B	D-PEPTIDE LINKING	C6 H13 N O2
DLY	B	D-PEPTIDE LINKING	C6 H14 N2 O2
DPN	B	D-PEPTIDE LINKING	C9 H11 N O2
DPR	B	D-PEPTIDE LINKING	C5 H9 N O2
DSG	B	D-PEPTIDE LINKING	C4 H8 N2 O3
DSN	B	D-PEPTIDE LINKING	C3 H7 N O3
DTH	B	D-PEPTIDE LINKING	C4 H9 N O3
DTY	B	D-PEPTIDE LINKING	C9 H11 N O3
DVA	B	D-PEPTIDE LINKING	C5 H11 N O2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.145 (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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Du, Q., Huang, Y.H., Wang, C.K., Craik, D.J.

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

Revision History  

• 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