PDB-9b26: Crystal structure of cod allergen Gad m 1.0201 coordinating lanthanum

ID or keywords:

Entry

Database: PDB / ID: 9b26

Title

Crystal structure of cod allergen Gad m 1.0201 coordinating lanthanum

Components

Parvalbumin beta

Keywords

ALLERGEN / parvalbumin / cod / allergy / lanthanum

Function / homology

Function and homology information

calcium ion binding / cytoplasm
Similarity search - Function

Biological species

Gadus morhua (Atlantic cod)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

O'Malley, A. / Chruszcz, M.

Funding support

1items

Citation

Journal: Protein Sci. / Year: 2024
Title: Comparative studies of seafood and reptile alpha- and beta-parvalbumins.
Authors: O'Malley, A. / Ray, J.M. / Kitlas, P. / Ruethers, T. / Kapingidza, A.B. / Cierpicki, T. / Lopata, A. / Kowal, K. / Chruszcz, M.

History

Deposition	Mar 14, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2025	Group: Database references / Category: citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9b26.cif.gz	75.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9b26.ent.gz	43.2 KB	Display	PDB format
PDBx/mmJSON format	9b26.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9b26_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	9b26_full_validation.pdf.gz	2.7 MB	Display
Data in XML	9b26_validation.xml.gz	10 KB	Display
Data in CIF	9b26_validation.cif.gz	13.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/9b26 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/9b26	HTTPS FTP

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Related structure data

Related structure data	9barC 9bb8C 9bcfC 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: Parvalbumin beta

hetero molecules

12.3 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)	46.712, 85.723, 54.786
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-204- LA
2	1	A-347- HOH
3	1	A-408- HOH
4	1	A-432- HOH
5	1	A-443- HOH
6	1	A-464- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Parvalbumin beta Mass: 11490.899 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gadus morhua (Atlantic cod) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90YK9

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Non-polymers , 5 types, 203 molecules

#2: Chemical	ChemComp-LA / LANTHANUM (III) ION Mass: 138.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.39 Å³/Da / Density % sol: 48.46 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.9 M sodium malonate pH 5.0

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→40 Å / Num. obs: 12683 / % possible obs: 92.8 % / Redundancy: 4.5 % / CC_1/2: 0.989 / R_merge(I) obs: 0.157 / R_pim(I) all: 0.084 / R_rim(I) all: 0.18 / R_sym value: 0.157 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.65→1.68 Å / R_merge(I) obs: 0.422 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 511 / CC_1/2: 0.745 / R_pim(I) all: 0.284 / R_rim(I) all: 0.515 / R_sym value: 0.422

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-2000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→33.781 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.646 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1967	637	5.041 %
R_work	0.1623	12000	-
all	0.164	-	-
obs	-	12637	92.851 %

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: 20.282 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.367 Å²	-0 Å²	0 Å²
2-	-	0.39 Å²	-0 Å²
3-	-	-	-0.756 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→33.781 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	808	0	17	196	1021

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	841
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	805
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.796	1127
X-RAY DIFFRACTION	r_angle_other_deg	0.532	1.789	1866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.167	5	111
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.452	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.518	10	147
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.217	10	36
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	125
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	970
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	174
X-RAY DIFFRACTION	r_nbd_refined	0.257	0.2	236
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	648
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	430
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	414
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	113
X-RAY DIFFRACTION	r_metal_ion_refined	0.114	0.2	22
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.388	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.129	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.182	0.2	39
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.141	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.118	1.766	441
X-RAY DIFFRACTION	r_mcbond_other	1.117	1.765	440
X-RAY DIFFRACTION	r_mcangle_it	1.568	3.178	550
X-RAY DIFFRACTION	r_mcangle_other	1.567	3.177	551
X-RAY DIFFRACTION	r_scbond_it	2.069	2.031	400
X-RAY DIFFRACTION	r_scbond_other	2.073	2.026	393
X-RAY DIFFRACTION	r_scangle_it	3.299	3.611	576
X-RAY DIFFRACTION	r_scangle_other	3.305	3.609	571
X-RAY DIFFRACTION	r_lrange_it	5.526	23.04	1119
X-RAY DIFFRACTION	r_lrange_other	5.219	18.773	1043

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
1.65-1.693	0.261	29	0.266	741	0.266	998	0.954	0.911	77.1543	0.241
1.693-1.739	0.242	34	0.217	844	0.218	959	0.967	0.969	91.5537	0.193
1.739-1.789	0.203	63	0.177	864	0.179	942	0.975	0.978	98.4076	0.15
1.789-1.844	0.186	53	0.175	836	0.175	895	0.975	0.978	99.3296	0.149
1.844-1.904	0.234	35	0.156	842	0.16	885	0.97	0.983	99.096	0.136
1.904-1.971	0.182	54	0.155	796	0.157	860	0.978	0.984	98.8372	0.137
1.971-2.045	0.202	43	0.148	769	0.151	831	0.98	0.987	97.7136	0.132
2.045-2.128	0.187	35	0.146	734	0.147	793	0.98	0.985	96.9735	0.133
2.128-2.223	0.234	32	0.153	708	0.157	779	0.966	0.983	94.9936	0.138
2.223-2.331	0.206	36	0.15	661	0.153	726	0.978	0.983	96.0055	0.137
2.331-2.456	0.167	38	0.158	624	0.159	693	0.98	0.983	95.5267	0.149
2.456-2.604	0.221	34	0.156	593	0.16	674	0.965	0.984	93.0267	0.157
2.604-2.783	0.173	19	0.151	554	0.152	617	0.979	0.985	92.8687	0.159
2.783-3.004	0.217	25	0.159	504	0.162	592	0.971	0.983	89.3581	0.176
3.004-3.288	0.296	23	0.179	438	0.184	545	0.936	0.979	84.5872	0.191
3.288-3.672	0.146	25	0.155	387	0.154	494	0.986	0.985	83.4008	0.182
3.672-4.232	0.189	16	0.149	354	0.15	445	0.981	0.986	83.1461	0.189
4.232-5.163	0.172	23	0.151	303	0.152	380	0.982	0.985	85.7895	0.196
5.163-7.217	0.204	15	0.188	267	0.189	304	0.972	0.976	92.7632	0.214
7.217-33.781	0.137	5	0.163	179	0.162	194	0.983	0.981	94.8454	0.206

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	2.4775	0.2295	-0.7368	0.6467	-0.5149	0.6514	-0.0392	0.1472	0.0756	-0.0562	0.0307	0.0011	0.0725	-0.0865	0.0085	0.0144	-0.0165	0.0028	0.0335	-0.0078	0.0181	-11.757	-12.001	-10.157
2	5.2638	2.0379	1.0924	1.3588	0.7176	1.631	-0.0398	-0.0709	-0.1127	-0.0139	-0.0249	-0.0573	0.1905	0.0355	0.0646	0.0366	0.0114	0.0096	0.0066	0.0016	0.0179	-4.085	-17.034	-4.829
3	0.6693	0.5135	-1.7311	4.2606	2.1894	7.7159	0.0441	-0.0103	-0.0237	0.072	0.0052	-0.2114	-0.0688	0.0418	-0.0493	0.0343	0.0209	-0.0074	0.0161	0.0055	0.1127	-3.851	-5.6	3.335
4	1.2514	0.1471	0.7407	0.8046	0.5501	1.492	0.0383	-0.1248	0.0295	0.1524	-0.0651	0.0203	0.0647	-0.0988	0.0268	0.0356	-0.0149	0.0094	0.0162	-0.0058	0.0079	-12.24	-13.629	4.034

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 26
2	X-RAY DIFFRACTION	2	ALL	A	27 - 45
3	X-RAY DIFFRACTION	3	ALL	A	46 - 57
4	X-RAY DIFFRACTION	4	ALL	A	58 - 109

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Protein , 1 types, 1 molecules A

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Non-polymers , 5 types, 203 molecules

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