PDB-8amc: Crystal Structure of cat allergen Fel d 4

ID or keywords:

Entry

Database: PDB / ID: 8amc

Title

Crystal Structure of cat allergen Fel d 4

Components

Allergen Fel d 4

Keywords

ALLERGEN / Lipocaline / cat allergene / lipocaline fold

Function / homology

Function and homology information

odorant binding / small molecule binding / extracellular space
Similarity search - Function

Biological species

Felis catus (domestic cat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

Schooltink, L. / Sagmeister, T. / Gottstein, N. / Pavkov-Keller, T. / Keller, W.

Funding support

Austria, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of cat allergen Fel d 4
Authors: Schooltink, L. / Sagmeister, T. / Gottstein, N. / Pavkov-Keller, T. / Keller, W.

History

Deposition	Aug 3, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2	Nov 13, 2024	Group: Structure summary Category: pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_contact_author.email / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8amc.cif.gz	261.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8amc.ent.gz	206 KB	Display	PDB format
PDBx/mmJSON format	8amc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8amc_validation.pdf.gz	465 KB	Display	wwPDB validaton report
Full document	8amc_full_validation.pdf.gz	467.5 KB	Display
Data in XML	8amc_validation.xml.gz	24.6 KB	Display
Data in CIF	8amc_validation.cif.gz	33.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/8amc ftp://data.pdbj.org/pub/pdb/validation_reports/am/8amc	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
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (5) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Allergen Fel d 4

B: Allergen Fel d 4

C: Allergen Fel d 4

D: Allergen Fel d 4

hetero molecules

89.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Allergen Fel d 4

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

2

B: Allergen Fel d 4

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

3

C: Allergen Fel d 4

hetero molecules

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

4

D: Allergen Fel d 4

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.291, 120.571, 67.149
Angle α, β, γ (deg.)	90.000, 106.513, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLU	GLU	GLY	GLY	A	A	4 - 161	26 - 183
2	2	1	GLU	GLU	GLY	GLY	B	B	4 - 161	26 - 183
3	3	2	ASN	ASN	ARG	ARG	A	A	5 - 160	27 - 182
4	4	2	ASN	ASN	ARG	ARG	C	C	5 - 160	27 - 182
5	5	3	ASN	ASN	ARG	ARG	A	A	5 - 160	27 - 182
6	6	3	ASN	ASN	ARG	ARG	D	D	5 - 160	27 - 182
7	7	4	ASN	ASN	ARG	ARG	B	B	5 - 160	27 - 182
8	8	4	ASN	ASN	ARG	ARG	C	C	5 - 160	27 - 182
9	9	5	ASN	ASN	ARG	ARG	B	B	5 - 160	27 - 182
10	10	5	ASN	ASN	ARG	ARG	D	D	5 - 160	27 - 182
11	11	6	ASN	ASN	GLY	GLY	C	C	5 - 161	27 - 183
12	12	6	ASN	ASN	GLY	GLY	D	D	5 - 161	27 - 183

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Allergen Fel d 4 Mass: 22277.926 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Felis catus (domestic cat) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5VFH6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.93 Å³/Da / Density % sol: 58.03 %
Crystal grow	Temperature: 293.15 K / Method: microbatch / pH: 4.5 Details: 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873128 Å / Relative weight: 1
Reflection	Resolution: 2.95→34.11 Å / Num. obs: 21622 / % possible obs: 99.61 % / Redundancy: 6.5 % / CC_1/2: 0.993 / R_merge(I) obs: 0.145 / R_pim(I) all: 0.094 / R_rim(I) all: 0.173 / Net I/σ(I): 9.8
Reflection shell	Resolution: 2.95→3.055 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.828 / Num. unique obs: 2177 / CC_1/2: 0.722 / R_pim(I) all: 0.523 / R_rim(I) all: 0.983

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
PHASER		phasing
Aimless		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 2.95→34.11 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.905 / SU B: 15.338 / SU ML: 0.279 / Cross valid method: FREE R-VALUE / ESU R Free: 0.349
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2299	1063	4.917 %
R_work	0.1787	20555	-
all	0.181	-	-
obs	-	21618	99.627 %

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: 62.645 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.904 Å²	0 Å²	0.59 Å²
2-	-	0.147 Å²	0 Å²
3-	-	-	0.347 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→34.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5138	0	10	99	5247

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	5246
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4972
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.158	0.01	16439
X-RAY DIFFRACTION	r_angle_refined_deg	1.74	1.634	7088
X-RAY DIFFRACTION	r_angle_other_deg	1.276	1.585	11458
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.159	5	626
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.722	23.566	286
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.905	15	960
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.978	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	674
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5850
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1198
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	645
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	3893
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	2345
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2308
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	63
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.792	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.524	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.773	0.2	6
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.584	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	5.62	6.33	2516
X-RAY DIFFRACTION	r_mcbond_other	5.612	6.327	2514
X-RAY DIFFRACTION	r_mcangle_it	8.867	9.48	3138
X-RAY DIFFRACTION	r_mcangle_other	8.859	9.48	3138
X-RAY DIFFRACTION	r_scbond_it	6.073	6.928	2730
X-RAY DIFFRACTION	r_scbond_other	6.052	6.913	2723
X-RAY DIFFRACTION	r_scangle_it	9.759	10.109	3950
X-RAY DIFFRACTION	r_scangle_other	9.725	10.086	3939
X-RAY DIFFRACTION	r_lrange_it	14.184	157.063	17339
X-RAY DIFFRACTION	r_lrange_other	14.173	157.082	17330
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.13	0.05	4429
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.134	0.05	4337
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.148	0.05	4313
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.136	0.05	4374
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.139	0.05	4337
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.128	0.05	4427

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.13	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.13	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13369	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.13369	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.148	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.148	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.1356	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.1356	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.13919	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.13919	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.12826	0.05009
6	12	D	X-RAY DIFFRACTION	Local ncs	0.12826	0.05009

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 (%)
2.95-3.026	0.363	64	0.338	1528	X-RAY DIFFRACTION	100
3.026-3.108	0.298	68	0.284	1467	X-RAY DIFFRACTION	100
3.108-3.198	0.282	61	0.245	1461	X-RAY DIFFRACTION	100
3.198-3.295	0.215	63	0.202	1388	X-RAY DIFFRACTION	100
3.295-3.402	0.257	72	0.21	1342	X-RAY DIFFRACTION	100
3.402-3.52	0.259	67	0.213	1306	X-RAY DIFFRACTION	99.9272
3.52-3.652	0.294	66	0.203	1253	X-RAY DIFFRACTION	99.8486
3.652-3.799	0.303	58	0.184	1219	X-RAY DIFFRACTION	99.61
3.799-3.966	0.215	65	0.168	1165	X-RAY DIFFRACTION	100
3.966-4.157	0.221	46	0.158	1119	X-RAY DIFFRACTION	99.7431
4.157-4.378	0.175	52	0.142	1057	X-RAY DIFFRACTION	99.6406
4.378-4.639	0.172	50	0.122	1005	X-RAY DIFFRACTION	99.9053
4.639-4.952	0.134	56	0.113	925	X-RAY DIFFRACTION	99.6951
4.952-5.34	0.165	85	0.122	854	X-RAY DIFFRACTION	99.6815
5.34-5.835	0.207	49	0.151	807	X-RAY DIFFRACTION	99.7669
5.835-6.5	0.252	44	0.187	735	X-RAY DIFFRACTION	100
6.5-7.461	0.323	46	0.209	655	X-RAY DIFFRACTION	99.7155
7.461-9.03	0.4	25	0.216	564	X-RAY DIFFRACTION	99.8305
9.03-12.345	0.228	19	0.156	437	X-RAY DIFFRACTION	97.4359

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