PDB-9fqf: Studies on chimeric PeAFB

ID or keywords:

Entry

Database: PDB / ID: 9fqf

Title

Studies on chimeric PeAFB

Components

Antifungal protein

Keywords

ANTIFUNGAL PROTEIN / PeAfpB / Penicillium expansum antifungal protein

Function / homology

Antifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / Antifungal protein

Function and homology information

Biological species

Penicillium expansum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.2 Å

Authors

Gallego del Sol, F. / Marina, A.

Funding support

Spain, 1items

Citation

Journal: To Be Published
Title: Studies on chimeric PeAFB
Authors: Gallego del Sol, F. / Marina, A.

History

Deposition	Jun 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fqf.cif.gz	75.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9fqf.ent.gz	46.3 KB	Display	PDB format
PDBx/mmJSON format	9fqf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/9fqf ftp://data.pdbj.org/pub/pdb/validation_reports/fq/9fqf	HTTPS FTP

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Related structure data

Related structure data	9fqgC 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

Deposited unit

A: Antifungal protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	45.963, 45.963, 41.891
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-229- HOH

#1: Protein	Antifungal protein Mass: 6708.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium expansum (fungus) / References: UniProt: A0A0A2K0J0
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.9 Å³/Da / Density % sol: 35.4 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6M ammonium sulfate, 1M Lithium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.97926 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection

Resolution: 1.2→41.89 Å / Num. obs: 16405 / % possible obs: 100 % / Redundancy: 18.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.027 / R_rim(I) all: 0.086 / Net I/σ(I): 21.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
6.57-41.89	16.1	0.059	16405	0.998	0.02	0.063
1.2-1.22	14.7	0.616	794	0.911	0.237	0.662

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
REFMAC	5.8.0425	refinement
Aimless		data scaling
autoPROC		data reduction
AutoProcess		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.2→39.805 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.969 / SU B: 0.849 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1452	809	4.939 %
R_work	0.1216	15571	-
all	0.123	-	-
obs	-	16380	99.982 %

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: 14.696 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.017 Å²	-0.009 Å²	-0 Å²
2-	-	-0.017 Å²	0 Å²
3-	-	-	0.057 Å²

Refinement step

Cycle: LAST / Resolution: 1.2→39.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	457	0	3	72	532

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	508
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	470
X-RAY DIFFRACTION	r_angle_refined_deg	1.873	1.905	687
X-RAY DIFFRACTION	r_angle_other_deg	0.901	1.912	1105
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.933	5	68
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.036	5	3
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.109	10	105
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.626	10	26
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	70
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	591
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	105
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	109
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	414
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	236
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	260
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.401	0.2	47
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.25	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.227	0.2	20
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.075	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.668	1.148	239
X-RAY DIFFRACTION	r_mcbond_other	3.663	1.15	240
X-RAY DIFFRACTION	r_mcangle_it	5.674	2.059	300
X-RAY DIFFRACTION	r_mcangle_other	5.681	2.061	301
X-RAY DIFFRACTION	r_scbond_it	5.482	1.526	269
X-RAY DIFFRACTION	r_scbond_other	5.472	1.526	270
X-RAY DIFFRACTION	r_scangle_it	8.093	2.643	381
X-RAY DIFFRACTION	r_scangle_other	8.083	2.642	382
X-RAY DIFFRACTION	r_lrange_it	13.86	19.377	633
X-RAY DIFFRACTION	r_lrange_other	13.038	17.317	612
X-RAY DIFFRACTION	r_rigid_bond_restr	3.974	3	978

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
1.2-1.231	0.138	46	0.131	1138	0.131	1186	0.99	0.989	99.8314	0.11
1.231-1.265	0.172	58	0.122	1095	0.124	1153	0.982	0.991	100	0.103
1.265-1.302	0.125	45	0.108	1084	0.109	1129	0.99	0.992	100	0.092
1.302-1.342	0.152	65	0.108	1044	0.111	1110	0.985	0.993	99.9099	0.091
1.342-1.385	0.12	60	0.103	1014	0.104	1074	0.991	0.994	100	0.09
1.385-1.434	0.101	62	0.095	956	0.095	1018	0.993	0.994	100	0.083
1.434-1.488	0.117	46	0.083	956	0.084	1002	0.991	0.996	100	0.073
1.488-1.549	0.113	45	0.086	924	0.087	969	0.991	0.995	100	0.077
1.549-1.618	0.11	66	0.088	843	0.09	909	0.992	0.995	100	0.083
1.618-1.696	0.12	45	0.09	860	0.092	905	0.992	0.995	100	0.086
1.696-1.788	0.124	49	0.101	778	0.102	827	0.989	0.994	100	0.098
1.788-1.896	0.115	46	0.102	774	0.103	820	0.992	0.994	100	0.101
1.896-2.027	0.115	23	0.113	730	0.113	753	0.993	0.993	100	0.115
2.027-2.189	0.135	39	0.118	671	0.119	710	0.99	0.992	100	0.126
2.189-2.397	0.171	23	0.122	630	0.124	653	0.981	0.991	100	0.13
2.397-2.678	0.14	23	0.144	567	0.144	590	0.987	0.988	100	0.164
2.678-3.091	0.185	18	0.134	517	0.136	535	0.98	0.989	100	0.16
3.091-3.779	0.116	21	0.125	437	0.125	458	0.993	0.991	100	0.152
3.779-5.321	0.233	22	0.146	340	0.15	362	0.978	0.989	100	0.178
5.321-39.805	0.326	7	0.254	213	0.256	220	0.957	0.96	100	0.299

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