PDB-8vqg: X-ray crystal structure of Can f 1

ID or keywords:

Entry

Database: PDB / ID: 8vqg

Title

X-ray crystal structure of Can f 1

Components

Major allergen Can f 1

Keywords

ALLERGEN / allergen-antibody complex / dog allergen Can f 1 / anti Can f 1 antibody / human IgE bound to Can f 1

Function / homology

von Ebner's gland protein/ Bos/Can allergen / Lipocalin / small molecule binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / extracellular space / MALONATE ION / Major allergen Can f 1

Function and homology information

Biological species

Canis lupus familiaris (dog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Khatri, K. / Geoffrey, M.A. / Pedersen, L.C. / Champan, M.D. / Pomes, A. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: X-ray crystal structure of natural Can f 1 in complex with human IgE 1J11 Fab
Authors: Khatri, K. / Ball, A. / Smith, S.A. / Champan, M.D. / Pomes, A. / Chruszcz, M.

History

Deposition	Jan 18, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8vqg.cif.gz	238.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8vqg.ent.gz		Display	PDB format
PDBx/mmJSON format	8vqg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vqg_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	8vqg_full_validation.pdf.gz	1 MB	Display
Data in XML	8vqg_validation.xml.gz	21.2 KB	Display
Data in CIF	8vqg_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/8vqg ftp://data.pdbj.org/pub/pdb/validation_reports/vq/8vqg	HTTPS FTP

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Related structure data

Related structure data	8vqfC 8epuS 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	#193 - Jan 2016 Siderocalin similarity (5) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Major allergen Can f 1

B: Major allergen Can f 1

C: Major allergen Can f 1

hetero molecules

49.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	85.494, 109.160, 127.764
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	29 - 174	3 - 148
2	1	1	GLN	GLN	29 - 174	3 - 148
3	2	2	SER	SER	29 - 170	3 - 144
4	2	2	SER	SER	29 - 170	3 - 144
5	3	3	SER	SER	29 - 170	3 - 144
6	3	3	SER	SER	29 - 170	3 - 144

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

#1: Protein	Major allergen Can f 1 / Allergen Dog 1 Mass: 16512.646 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: O18873
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₂O₄ / Feature type: SUBJECT OF INVESTIGATION
#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	Y
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: 3.01 Å³/Da / Density % sol: 59.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5 M sodium malonate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→40 Å / Num. obs: 20197 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.036 / R_rim(I) all: 0.097 / R_sym value: 0.09 / Net I/σ(I): 24.3
Reflection shell	Resolution: 2.55→2.59 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.623 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1005 / CC_1/2: 0.811 / CC star: 0.946 / R_pim(I) all: 0.258 / R_rim(I) all: 0.676 / R_sym value: 0.623 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 8EPU

8epu

Resolution: 2.55→36.015 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.915 / SU B: 23.149 / SU ML: 0.244 / Cross valid method: FREE R-VALUE / ESU R: 0.493 / ESU R Free: 0.291
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2596	1009	5.092 %
R_work	0.2218	18805	-
all	0.224	-	-
obs	-	19814	99.834 %

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: 60.723 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.977 Å²	-0 Å²	0 Å²
2-	-	3.23 Å²	-0 Å²
3-	-	-	-2.254 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→36.015 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3376	0	21	99	3496

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	3467
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3271
X-RAY DIFFRACTION	r_angle_refined_deg	1.137	1.85	4688
X-RAY DIFFRACTION	r_angle_other_deg	0.421	1.765	7559
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.229	5	434
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.129	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.629	10	614
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.981	10	160
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	513
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4116
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	750
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	525
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	2855
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	1595
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1757
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.106	0.2	132
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.187	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.084	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	1.206	4.135	1742
X-RAY DIFFRACTION	r_mcbond_other	1.206	4.135	1742
X-RAY DIFFRACTION	r_mcangle_it	2.191	7.443	2174
X-RAY DIFFRACTION	r_mcangle_other	2.191	7.444	2175
X-RAY DIFFRACTION	r_scbond_it	1.056	4.25	1725
X-RAY DIFFRACTION	r_scbond_other	1.053	4.246	1722
X-RAY DIFFRACTION	r_scangle_it	1.76	7.795	2514
X-RAY DIFFRACTION	r_scangle_other	1.759	7.796	2515
X-RAY DIFFRACTION	r_lrange_it	3.747	39.502	3507
X-RAY DIFFRACTION	r_lrange_other	3.708	39.34	3494
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.132	0.05	4044
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.131	0.05	4022
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.147	0.05	3985

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	0.13181	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13181	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13059	0.05007
2	4	A	X-RAY DIFFRACTION	Local ncs	0.13059	0.05007
3	5	A	X-RAY DIFFRACTION	Local ncs	0.14655	0.05007
3	6	A	X-RAY DIFFRACTION	Local ncs	0.14655	0.05007

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
2.55-2.616	0.338	64	0.374	1342	0.372	1415	0.927	0.923	99.364	0.346
2.616-2.687	0.293	67	0.323	1351	0.322	1419	0.954	0.937	99.9295	0.297
2.687-2.765	0.323	84	0.299	1279	0.3	1363	0.943	0.946	100	0.268
2.765-2.849	0.316	60	0.275	1272	0.277	1333	0.927	0.952	99.925	0.243
2.849-2.942	0.305	64	0.274	1210	0.275	1275	0.944	0.949	99.9216	0.242
2.942-3.045	0.363	63	0.26	1202	0.264	1265	0.921	0.956	100	0.236
3.045-3.159	0.315	66	0.246	1145	0.25	1212	0.942	0.961	99.9175	0.228
3.159-3.287	0.35	55	0.251	1099	0.255	1156	0.91	0.961	99.827	0.229
3.287-3.431	0.335	49	0.233	1066	0.238	1116	0.938	0.967	99.9104	0.216
3.431-3.597	0.242	42	0.222	1018	0.223	1060	0.967	0.97	100	0.208
3.597-3.79	0.245	54	0.215	966	0.216	1020	0.964	0.972	100	0.205
3.79-4.017	0.249	57	0.209	924	0.211	984	0.965	0.973	99.6951	0.198
4.017-4.29	0.228	48	0.19	868	0.192	917	0.962	0.977	99.8909	0.188
4.29-4.629	0.195	53	0.17	797	0.172	852	0.978	0.982	99.7653	0.173
4.629-5.062	0.167	42	0.155	744	0.156	786	0.983	0.985	100	0.16
5.062-5.646	0.293	47	0.212	677	0.216	724	0.948	0.974	100	0.214
5.646-6.492	0.216	38	0.228	611	0.228	649	0.969	0.971	100	0.232
6.492-7.888	0.31	23	0.213	533	0.217	557	0.95	0.972	99.8205	0.219
7.888-10.897	0.212	18	0.181	426	0.182	445	0.974	0.98	99.7753	0.197
10.897-36.015	0.233	15	0.233	272	0.233	287	0.948	0.965	100	0.258

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.1497	0.7756	0.4345	4.8337	-0.3798	2.538	-0.1378	0.2896	0.0721	-0.4552	0.4743	0.3496	0.2633	-0.2903	-0.3365	0.0781	-0.0836	-0.0745	0.2622	0.0513	0.0806	-37.158	-8.662	-15.387
2	6.1434	-3.5527	1.098	2.5599	-1.5214	3.6563	0.5072	0.5334	0.2035	-0.6556	-0.4983	-0.1217	0.6492	0.4771	-0.009	0.3534	0.2016	0.0667	0.1571	0.0225	0.0601	-11.521	-22.215	-6.956
3	3.4576	0.2237	-1.1429	1.7529	-0.0823	3.9038	0.1381	-0.5008	-0.0695	0.3834	-0.2558	-0.0486	0.2575	0.058	0.1177	0.1353	-0.1101	0.0078	0.1515	-0.0049	0.0153	-30.018	-19.586	22.88

Refinement TLS group

Selection: ALL

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