5E5Y | pdb_00005e5y

Quasi-racemic snakin-1 in P1 before radiation damage

PDB DOI: https://doi.org/10.2210/pdb5E5Y/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Solanum tuberosum
Mutation(s): Yes

Deposited: 2015-10-09 Released: 2016-05-18
Deposition Author(s): Yeung, H., Squire, C.J., Yosaatmadja, Y., Panjikar, S., Baker, E.N., Harris, P.W.R., Brimble, M.A.
Funding Organization(s): Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.226 (Depositor), 0.227 (DCC)
R-Value Work:
0.179 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily.

Yeung, H., Squire, C.J., Yosaatmadja, Y., Panjikar, S., Lopez, G., Molina, A., Baker, E.N., Harris, P.W., Brimble, M.A.

(2016) Angew Chem Int Ed Engl 55: 7930-7933

PubMed: 27145301 Search on PubMed
DOI: https://doi.org/10.1002/anie.201602719
Primary Citation Related Structures:
5E5Q, 5E5T, 5E5Y

PubMed Abstract:
Proteins from the GASA/snakin superfamily are common in plant proteomes and have diverse functions, including hormonal crosstalk, development, and defense. One 63-residue member of this family, snakin-1, an antimicrobial protein from potatoes, has previously been chemically synthesized in a fully active form. Herein the 1.5 Å structure of snakin-1, determined by a novel combination of racemic protein crystallization and radiation-damage-induced phasing (RIP), is reported. Racemic crystals of snakin-1 and quasi-racemic crystals incorporating an unnatural 4-iodophenylalanine residue were prepared from chemically synthesized d- and l-proteins. Breakage of the C-I bonds in the quasi-racemic crystals facilitated structure determination by RIP. The crystal structure reveals a unique protein fold with six disulfide crosslinks, presenting a distinct electrostatic surface that may target the protein to microbial cell surfaces.

Organizational Affiliation

School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland Central, 1010, New Zealand.

Macromolecule Content

Total Structure Weight: 28.58 kDa
Atom Count: 2,220
Modeled Residue Count: 251
Deposited Residue Count: 252
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snakin-1	A, C	63	Solanum tuberosum	Mutation(s): 1
UniProt
Find proteins for Q948Z4 (Solanum tuberosum) Explore Q948Z4 Go to UniProtKB: Q948Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q948Z4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D- snakin-1	B, D	63	Solanum tuberosum	Mutation(s): 0
UniProt
Find proteins for Q948Z4 (Solanum tuberosum) Explore Q948Z4 Go to UniProtKB: Q948Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q948Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	E [auth A], F [auth A], H [auth B], K [auth C], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	G [auth B] I [auth C] J [auth C] L [auth D] M [auth D] G [auth B], I [auth C], J [auth C], L [auth D], M [auth D], N [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHI Query on PHI	A, C	L-PEPTIDE LINKING	C₉ H₁₀ I N O₂		PHE
DAL Query on DAL	B, D	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DAR Query on DAR	B, D	D-PEPTIDE LINKING	C₆ H₁₅ N₄ O₂		--
DAS Query on DAS	B, D	D-PEPTIDE LINKING	C₄ H₇ N O₄		--
DCY Query on DCY	B, D	D-PEPTIDE LINKING	C₃ H₇ N O₂ S		--
DGL Query on DGL	B, D	D-PEPTIDE LINKING	C₅ H₉ N O₄		--
DHI Query on DHI	B, D	D-PEPTIDE LINKING	C₆ H₁₀ N₃ O₂		--
DIL Query on DIL	B, D	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DLE Query on DLE	B, D	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DLY Query on DLY	B, D	D-PEPTIDE LINKING	C₆ H₁₄ N₂ O₂		--
DPN Query on DPN	B, D	D-PEPTIDE LINKING	C₉ H₁₁ N O₂		--
DPR Query on DPR	B, D	D-PEPTIDE LINKING	C₅ H₉ N O₂		--
DSG Query on DSG	B, D	D-PEPTIDE LINKING	C₄ H₈ N₂ O₃		--
DSN Query on DSN	B, D	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
DTH Query on DTH	B, D	D-PEPTIDE LINKING	C₄ H₉ N O₃		--
DTY Query on DTY	B, D	D-PEPTIDE LINKING	C₉ H₁₁ N O₃		--
DVA Query on DVA	B, D	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.226 (Depositor), 0.227 (DCC)
R-Value Work: 0.179 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.233	α = 93
b = 37.415	β = 90.58
c = 50.303	γ = 102.57

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
SHELXDE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	UOA1115

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2016-07-20
Changes: Database references
Version 1.2: 2025-04-02
Changes: Data collection, Database references, Derived calculations, Structure summary