PDB-9hvn: Atomic resolution crystal structure of the hexameric antimicrobia...

ID or keywords:

Entry

Database: PDB / ID: 9hvn

Title

Atomic resolution crystal structure of the hexameric antimicrobial peptide Magainin-2

Components

Magainins

Keywords

ANTIBIOTIC / Antimicrobial peptide / peptide channel / atomic resolution

Function / homology

antimicrobial peptide biosynthetic process / extraorganismal space / regulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / Magainins

Function and homology information

Biological species

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.05 Å

Authors

Zeth, K. / Sancho-Vaello, E.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure and mechanism of the hexameric peptide structure of Magainin-2
Authors: Zeth, K. / Sancho-Vaello, E.

History

Deposition	Dec 31, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hvn.cif.gz	26.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9hvn.ent.gz	13.1 KB	Display	PDB format
PDBx/mmJSON format	9hvn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hvn_validation.pdf.gz	422.4 KB	Display	wwPDB validaton report
Full document	9hvn_full_validation.pdf.gz	422.3 KB	Display
Data in XML	9hvn_validation.xml.gz	3.3 KB	Display
Data in CIF	9hvn_validation.cif.gz	3.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hv/9hvn ftp://data.pdbj.org/pub/pdb/validation_reports/hv/9hvn	HTTPS FTP

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Related structure data

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

Deposited unit

A: Magainins

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

1

A: Magainins

x 6

defined by software
Evidence: cross-linking
14.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	10_555	-y,-x,-z+1/2	1
crystal symmetry operation	11_555	-x+y,y,-z+1/2	1
crystal symmetry operation	12_555	x,x-y,-z+1/2	1

Unit cell

Length a, b, c (Å)	34.359, 34.359, 55.795
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-103- HOH
2	1	A-108- HOH

#1: Protein/peptide	Magainins Mass: 2471.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: P11006
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 36.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 35% MPD, 20 mM HEPES, pH 7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.05→29.76 Å / Num. obs: 9455 / % possible obs: 97.81 % / Redundancy: 8.1 % / CC_1/2: 0.99 / R_merge(I) obs: 0.029 / Net I/σ(I): 27.36
Reflection shell	Resolution: 1.05→1.077 Å / Redundancy: 4.35 % / R_merge(I) obs: 0.92 / Num. unique obs: 576 / CC_1/2: 0.51

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
XSCALE		data scaling
BUCCANEER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.05→29.756 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.958 / SU B: 0.898 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.177	946	10.005 %
R_work	0.1674	8509	-
all	0.168	-	-
obs	-	9455	97.807 %

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: 22.402 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.035 Å²	-0.017 Å²	-0 Å²
2-	-	-0.035 Å²	0 Å²
3-	-	-	0.113 Å²

Refinement step

Cycle: LAST / Resolution: 1.05→29.756 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	168	0	0	10	178

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	199
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	206
X-RAY DIFFRACTION	r_angle_refined_deg	1.553	1.622	266
X-RAY DIFFRACTION	r_angle_other_deg	0.515	1.593	479
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.448	5	25
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.358	10	42
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	10.873	10	8
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	27
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	226
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	46
X-RAY DIFFRACTION	r_nbd_refined	0.243	0.2	43
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.169	0.2	157
X-RAY DIFFRACTION	r_nbtor_refined	0.21	0.2	95
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.065	0.2	112
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.022	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.29	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.322	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.287	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.756	1.842	99
X-RAY DIFFRACTION	r_mcbond_other	1.755	1.868	100
X-RAY DIFFRACTION	r_mcangle_it	2.5	3.317	124
X-RAY DIFFRACTION	r_mcangle_other	2.172	3.27	123
X-RAY DIFFRACTION	r_scbond_it	2.329	2.563	100
X-RAY DIFFRACTION	r_scbond_other	2.32	2.583	101
X-RAY DIFFRACTION	r_scangle_it	3.189	4.372	139
X-RAY DIFFRACTION	r_scangle_other	3.178	4.389	140
X-RAY DIFFRACTION	r_lrange_it	5.02	24.353	723
X-RAY DIFFRACTION	r_lrange_other	5.002	24.351	722
X-RAY DIFFRACTION	r_rigid_bond_restr	5.667	3	405

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.05-1.077	0.303	64	0.325	576	0.323	706	0.907	0.908	90.6516	0.308
1.077-1.107	0.263	64	0.282	578	0.28	673	0.949	0.936	95.3938	0.247
1.107-1.139	0.221	64	0.212	577	0.213	647	0.963	0.967	99.0726	0.173
1.139-1.174	0.227	63	0.169	570	0.174	633	0.962	0.976	100	0.129
1.174-1.212	0.187	63	0.165	562	0.167	625	0.977	0.977	100	0.12
1.212-1.255	0.173	60	0.145	537	0.148	600	0.977	0.983	99.5	0.108
1.255-1.302	0.128	58	0.121	526	0.121	584	0.99	0.99	100	0.085
1.302-1.355	0.137	55	0.11	493	0.113	549	0.988	0.992	99.8178	0.083
1.355-1.415	0.141	55	0.124	494	0.125	550	0.989	0.989	99.8182	0.095
1.415-1.484	0.147	52	0.114	468	0.118	526	0.987	0.992	98.8593	0.097
1.484-1.564	0.142	49	0.11	446	0.113	498	0.987	0.992	99.3976	0.095
1.564-1.659	0.133	46	0.108	414	0.111	464	0.988	0.992	99.1379	0.095
1.659-1.773	0.18	45	0.11	401	0.116	453	0.98	0.992	98.4547	0.098
1.773-1.914	0.142	42	0.131	374	0.132	424	0.988	0.989	98.1132	0.122
1.914-2.096	0.195	37	0.141	338	0.146	383	0.978	0.987	97.9112	0.131
2.096-2.342	0.13	35	0.131	321	0.131	367	0.989	0.989	97.0027	0.132
2.342-2.702	0.108	31	0.145	274	0.141	317	0.995	0.989	96.2145	0.163
2.702-3.302	0.157	28	0.18	241	0.178	283	0.983	0.979	95.053	0.193
3.302-4.641	0.256	20	0.201	194	0.205	231	0.963	0.97	92.6407	0.248
4.641-29.756	0.253	15	0.295	125	0.291	154	0.926	0.94	90.9091	0.353

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