PDB-9bar: Crystal structure of the alpha parvalbumin from thornback ray

ID or keywords:

Entry

Database: PDB / ID: 9bar

Title

Crystal structure of the alpha parvalbumin from thornback ray

Components

Parvalbumin alpha

Keywords

ALLERGEN / parvalbumin / thornback ray / allergy

Function / homology

Function and homology information

calcium ion binding / cytoplasm
Similarity search - Function

Biological species

Raja clavata (thornback ray)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

O'Malley, A. / Kapingidza, A.B. / Ruethers, T. / Lopata, A.L. / 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	Apr 4, 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	9bar.cif.gz	75.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bar.ent.gz	41.9 KB	Display	PDB format
PDBx/mmJSON format	9bar.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9bar_validation.pdf.gz	429.4 KB	Display	wwPDB validaton report
Full document	9bar_full_validation.pdf.gz	429.3 KB	Display
Data in XML	9bar_validation.xml.gz	8.6 KB	Display
Data in CIF	9bar_validation.cif.gz	11.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ba/9bar ftp://data.pdbj.org/pub/pdb/validation_reports/ba/9bar	HTTPS FTP

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Related structure data

Related structure data	9b26C 9bb8C 9bcfC 5zh6S 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

Deposited unit

A: Parvalbumin alpha

hetero molecules

13.9 kDa, 1 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)	32.199, 37.725, 38.809
Angle α, β, γ (deg.)	90.000, 95.369, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Parvalbumin alpha Mass: 13663.187 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Raja clavata (thornback ray) / Production host: Escherichia coli (E. coli) / References: UniProt: P02630
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.72 Å³/Da / Density % sol: 28.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 2.5 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→40 Å / Num. obs: 9078 / % possible obs: 95 % / Redundancy: 3.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.091 / R_pim(I) all: 0.058 / R_rim(I) all: 0.108 / R_sym value: 0.091 / Net I/σ(I): 18.7
Reflection shell	Resolution: 1.75→1.78 Å / R_merge(I) obs: 0.392 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 462 / CC_1/2: 0.85 / R_pim(I) all: 0.259 / R_rim(I) all: 0.478 / R_sym value: 0.392

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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
Starting model: PDB entry 5ZH6

5zh6

Resolution: 1.75→32.078 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.929 / SU B: 5.781 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2228	415	4.601 %
R_work	0.1824	8604	-
all	0.184	-	-
obs	-	9019	95.037 %

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: 17.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.577 Å²	-0 Å²	-0.356 Å²
2-	-	0.642 Å²	0 Å²
3-	-	-	0.985 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→32.078 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	821	0	12	118	951

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	891
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	841
X-RAY DIFFRACTION	r_angle_refined_deg	1.264	1.807	1209
X-RAY DIFFRACTION	r_angle_other_deg	0.491	1.786	1963
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.672	5	123
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.82	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.034	10	166
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.319	10	39
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	137
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1037
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	187
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	229
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	678
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	446
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	395
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	75
X-RAY DIFFRACTION	r_metal_ion_refined	0.133	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.227	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.218	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.232	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	0.949	1.397	453
X-RAY DIFFRACTION	r_mcbond_other	0.948	1.397	453
X-RAY DIFFRACTION	r_mcangle_it	1.57	2.499	571
X-RAY DIFFRACTION	r_mcangle_other	1.569	2.501	572
X-RAY DIFFRACTION	r_scbond_it	1.385	1.644	438
X-RAY DIFFRACTION	r_scbond_other	1.379	1.579	431
X-RAY DIFFRACTION	r_scangle_it	2.353	2.934	632
X-RAY DIFFRACTION	r_scangle_other	2.355	2.812	621
X-RAY DIFFRACTION	r_lrange_it	5.081	18.672	1117
X-RAY DIFFRACTION	r_lrange_other	4.619	15.331	1075

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
1.75-1.795	0.373	29	0.279	642	0.283	702	0.933	0.951	95.584	0.254
1.795-1.844	0.18	21	0.229	626	0.228	670	0.965	0.967	96.5672	0.207
1.844-1.898	0.318	32	0.212	624	0.218	660	0.936	0.971	99.3939	0.186
1.898-1.956	0.262	35	0.209	585	0.212	625	0.954	0.967	99.2	0.182
1.956-2.02	0.185	32	0.17	595	0.17	630	0.98	0.98	99.5238	0.155
2.02-2.09	0.26	36	0.181	546	0.186	594	0.961	0.98	97.9798	0.16
2.09-2.169	0.197	23	0.164	554	0.166	585	0.97	0.984	98.6325	0.151
2.169-2.257	0.225	31	0.163	524	0.167	567	0.966	0.982	97.8836	0.149
2.257-2.357	0.283	24	0.17	492	0.175	531	0.955	0.982	97.1751	0.156
2.357-2.471	0.154	27	0.162	455	0.161	513	0.981	0.984	93.9571	0.154
2.471-2.604	0.26	17	0.177	421	0.18	479	0.961	0.98	91.4405	0.172
2.604-2.761	0.192	18	0.181	428	0.182	464	0.975	0.98	96.1207	0.174
2.761-2.95	0.205	24	0.179	384	0.181	436	0.979	0.979	93.578	0.175
2.95-3.184	0.215	18	0.169	364	0.171	416	0.968	0.982	91.8269	0.17
3.184-3.484	0.341	13	0.186	310	0.192	368	0.925	0.979	87.7717	0.195
3.484-3.89	0.139	9	0.164	280	0.163	347	0.99	0.982	83.2853	0.18
3.89-4.481	0.256	5	0.159	242	0.161	307	0.967	0.984	80.456	0.189
4.481-5.461	0.07	6	0.191	222	0.187	262	0.996	0.98	87.0229	0.219
5.461-7.614	0.27	9	0.231	190	0.233	203	0.961	0.97	98.0296	0.252
7.614-32.078	0.174	6	0.179	118	0.178	127	0.985	0.979	97.6378	0.21

Refinement TLS params.

Method: refined / Origin x: 0.4646 Å / Origin y: -0.6658 Å / Origin z: 10.4889 Å

	11	12	13	21	22	23	31	32	33
T	0.0186 Å²	0.0105 Å²	0.0077 Å²	-	0.0137 Å²	-0.003 Å²	-	-	0.014 Å²
L	0.628 °²	0.2149 °²	0.1971 °²	-	0.9503 °²	-0.7127 °²	-	-	1.0689 °²
S	0.023 Å °	0.0726 Å °	-0.0417 Å °	0.0111 Å °	-0.0122 Å °	0.0282 Å °	0.0084 Å °	0.0536 Å °	-0.0108 Å °

Refinement TLS group

Selection: ALL

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