PDB-7o76: Reversible supramolecular assembly of the anti-microbial peptide ...

ID or keywords:

Entry

Database: PDB / ID: 7o76

Title

Reversible supramolecular assembly of the anti-microbial peptide plectasin

Components

Fungal defensin plectasin

Keywords

ANTIMICROBIAL PROTEIN / fungal defensin

Function / homology

Function and homology information

potassium channel regulator activity / toxin activity / defense response to bacterium / host cell plasma membrane / extracellular region / membrane
Similarity search - Function

Biological species

Pseudoplectania nigrella (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.131 Å

Authors

Pohl, C. / Noergaard, N. / Harris, P.

Funding support

European Union, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils.
Authors: Christin Pohl / Gregory Effantin / Eaazhisai Kandiah / Sebastian Meier / Guanghong Zeng / Werner Streicher / Dorotea Raventos Segura / Per H Mygind / Dorthe Sandvang / Line Anker Nielsen / ...
Abstract: Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of ...

History

Deposition	Apr 13, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 29, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7o76.cif.gz	43.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7o76.ent.gz		Display	PDB format
PDBx/mmJSON format	7o76.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7o76_validation.pdf.gz	438.4 KB	Display	wwPDB validaton report
Full document	7o76_full_validation.pdf.gz	438.8 KB	Display
Data in XML	7o76_validation.xml.gz	4.4 KB	Display
Data in CIF	7o76_validation.cif.gz	5.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o7/7o76 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/7o76	HTTPS FTP

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Related structure data

Related structure data	12775C 12776C 7oaeC 7oagC 3e7uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#199 - Jul 2016 Monellin similarity (1) #38 - Feb 2003 Potassium Channels similarity (1)

Deposited unit

XXX: Fungal defensin plectasin

hetero molecules

4.52 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	23.678, 20.093, 32.546
Angle α, β, γ (deg.)	90.000, 104.279, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein/peptide	Fungal defensin plectasin Mass: 4415.024 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoplectania nigrella (fungus) / Gene: DEF / Production host: Aspergillus oryzae (mold) / References: UniProt: Q53I06
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.7 Å³/Da / Density % sol: 27.62 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 15 mg/mL plectasin in 10 mM His pH 4.5 added to a reservoir of 0.1 M NH4Ac, 0.1 M Tris pH 8.5 and 40% isopropanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97247 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2020 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)
Radiation	Monochromator: Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97247 Å / Relative weight: 1
Reflection	Resolution: 1.13→31.53 Å / Num. obs: 10216 / % possible obs: 89.9 % / Redundancy: 6 % / CC_1/2: 0.999 / Net I/σ(I): 22.49
Reflection shell	Resolution: 1.13→1.2 Å / Num. unique obs: 1020 / CC_1/2: 0.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3E7U

3e7u

Resolution: 1.131→21.219 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.976 / WR_factor R_free: 0.215 / WR_factor R_work: 0.164 / SU B: 2.377 / SU ML: 0.045 / Average fsc free: 0.9365 / Average fsc work: 0.9497 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.1781	507	4.963 %
R_work	0.1457	9708	-
all	0.147	-	-
obs	-	10215	90.231 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.922 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.945 Å²	-0 Å²	1.224 Å²
2-	-	-2.283 Å²	-0 Å²
3-	-	-	-1.137 Å²

Refinement step

Cycle: LAST / Resolution: 1.131→21.219 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	305	0	7	24	336

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.012	342
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.018	280
X-RAY DIFFRACTION	r_angle_refined_deg	1.965	1.639	457
X-RAY DIFFRACTION	r_angle_other_deg	0.686	1.606	658
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.441	5	43
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.955	24.375	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.952	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	35
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	403
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	81
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	69
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.244	0.2	255
X-RAY DIFFRACTION	r_nbtor_refined	0.208	0.2	160
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.098	0.2	139
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	15
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.261	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.255	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	2.667	2.271	166
X-RAY DIFFRACTION	r_mcbond_other	2.671	2.27	165
X-RAY DIFFRACTION	r_mcangle_it	3.414	3.427	208
X-RAY DIFFRACTION	r_mcangle_other	3.406	3.427	209
X-RAY DIFFRACTION	r_scbond_it	7.27	2.931	176
X-RAY DIFFRACTION	r_scbond_other	7.005	2.895	170
X-RAY DIFFRACTION	r_scangle_it	7.73	4.143	248
X-RAY DIFFRACTION	r_scangle_other	7.495	4.105	243
X-RAY DIFFRACTION	r_lrange_it	7.751	28.877	388
X-RAY DIFFRACTION	r_lrange_other	6.994	27.986	381
X-RAY DIFFRACTION	r_rigid_bond_restr	6.438	3	622

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.131-1.16	0.398	18	0.385	341	X-RAY DIFFRACTION	43.3575
1.16-1.192	0.321	25	0.302	495	X-RAY DIFFRACTION	64.0394
1.192-1.227	0.223	36	0.25	572	X-RAY DIFFRACTION	78.2497
1.227-1.264	0.278	39	0.216	638	X-RAY DIFFRACTION	88.3812
1.264-1.306	0.176	29	0.181	705	X-RAY DIFFRACTION	98.9218
1.306-1.351	0.198	35	0.177	686	X-RAY DIFFRACTION	99.8615
1.351-1.402	0.21	36	0.161	645	X-RAY DIFFRACTION	100
1.402-1.459	0.15	27	0.148	630	X-RAY DIFFRACTION	99.848
1.459-1.524	0.181	26	0.149	611	X-RAY DIFFRACTION	99.8433
1.524-1.598	0.195	30	0.129	591	X-RAY DIFFRACTION	99.679
1.598-1.685	0.193	26	0.123	561	X-RAY DIFFRACTION	99.8299
1.685-1.787	0.174	30	0.132	516	X-RAY DIFFRACTION	100
1.787-1.909	0.241	21	0.122	500	X-RAY DIFFRACTION	100
1.909-2.062	0.196	27	0.125	460	X-RAY DIFFRACTION	99.1853
2.062-2.258	0.199	23	0.124	419	X-RAY DIFFRACTION	98.6607
2.258-2.523	0.136	21	0.133	387	X-RAY DIFFRACTION	99.7555
2.523-2.91	0.203	25	0.141	342	X-RAY DIFFRACTION	99.458
2.91-3.556	0.213	13	0.147	292	X-RAY DIFFRACTION	99.3485
3.556-4.997	0.111	15	0.137	210	X-RAY DIFFRACTION	90.7258
4.997-10	0.205	5	0.254	107	X-RAY DIFFRACTION	76.1905

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