7RIH | pdb_00007rih

hyen D

• PDB DOI: https://doi.org/10.2210/pdb7RIH/pdb

• Classification: PLANT PROTEIN
• Organism(s): Pigea enneasperma
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (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 and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 6.74 kDa 
• Atom Count: 543 
• Modeled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-[I11L]hyen D	A	30	Pigea enneasperma	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclotide hyen-D	B	30	Pigea enneasperma	Mutation(s): 0
UniProt
Find proteins for C0HLN8 (Pigea enneasperma) Explore C0HLN8  Go to UniProtKB:  C0HLN8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A], D [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.038	α = 90
b = 24.731	β = 102.47
c = 34.729	γ = 90

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., Craik, D.J., Wang, C.K.

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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, Derived calculations
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-09
  Changes: Structure summary