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), 0.224 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.224 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (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

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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

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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.