PDB-8ti6: Crystal structure of Tyr p 36.0101

ID or keywords:

Entry

Database: PDB / ID: 8ti6

Title

Crystal structure of Tyr p 36.0101

Components

Profilin
Proline-rich peptide

Keywords

ALLERGEN / mite profilin / storage mite / allergy

Function / homology

Function and homology information

sequestering of actin monomers / actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function

Biological species

Tyrophagus putrescentiae (arthropod)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 Å

Authors

O'Malley, A. / Sankaran, S. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: Biol.Chem. / Year: 2024
Title: Structural homology of mite profilins to plant profilins is not indicative of allergic cross-reactivity.
Authors: O'Malley, A. / Sankaran, S. / Carriuolo, A. / Khatri, K. / Kowal, K. / Chruszcz, M.

History

Deposition	Jul 19, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ti6.cif.gz	94.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ti6.ent.gz	54.3 KB	Display	PDB format
PDBx/mmJSON format	8ti6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ti6_validation.pdf.gz	445.7 KB	Display	wwPDB validaton report
Full document	8ti6_full_validation.pdf.gz	446 KB	Display
Data in XML	8ti6_validation.xml.gz	8.6 KB	Display
Data in CIF	8ti6_validation.cif.gz	11.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ti/8ti6 ftp://data.pdbj.org/pub/pdb/validation_reports/ti/8ti6	HTTPS FTP

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Related structure data

Related structure data	8ti5C 8ti7C 8v5yC 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	#19 - Jul 2001 Actin similarity (6)

Deposited unit

A: Profilin

B: Proline-rich peptide

hetero molecules

18 kDa, 2 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)	54.974, 54.974, 79.315
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Profilin Mass: 16881.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tyrophagus putrescentiae (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2YLJ4
#2: Protein/peptide	Proline-rich peptide Mass: 1032.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.04 Å³/Da / Density % sol: 39.64 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid pH 4.0, 0.8 M ammonium sulfate

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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: Jul 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.42→40 Å / Num. obs: 25963 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 10 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.018 / R_rim(I) all: 0.06 / R_sym value: 0.057 / Net I/σ(I): 38.9
Reflection shell	Resolution: 1.42→1.44 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.309 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 982 / CC_1/2: 0.889 / CC star: 0.97 / R_pim(I) all: 0.171 / R_rim(I) all: 0.358 / R_sym value: 0.309 / % possible all: 72.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.42→30.49 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.973 / SU B: 1.697 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.154	1219	4.703 %
R_work	0.1331	24703	-
all	0.134	-	-
obs	-	25922	96.782 %

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: 15.173 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.157 Å²	0.079 Å²	0 Å²
2-	-	0.157 Å²	-0 Å²
3-	-	-	-0.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.42→30.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	994	0	5	110	1109

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	1133
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1084
X-RAY DIFFRACTION	r_angle_refined_deg	1.63	1.643	1559
X-RAY DIFFRACTION	r_angle_other_deg	0.65	1.578	2504
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.533	5	158
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.674	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.685	10	194
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.24	10	52
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	176
X-RAY DIFFRACTION	r_chiral_restr_other	0.262	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1409
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	267
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	196
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	929
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	516
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	608
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.056	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.167	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.293	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.985	1.365	575
X-RAY DIFFRACTION	r_mcbond_other	0.98	1.364	575
X-RAY DIFFRACTION	r_mcangle_it	1.422	2.434	731
X-RAY DIFFRACTION	r_mcangle_other	1.427	2.444	732
X-RAY DIFFRACTION	r_scbond_it	1.273	1.737	558
X-RAY DIFFRACTION	r_scbond_other	1.271	1.743	559
X-RAY DIFFRACTION	r_scangle_it	1.707	3.039	821
X-RAY DIFFRACTION	r_scangle_other	1.706	3.045	822
X-RAY DIFFRACTION	r_lrange_it	2.436	17.627	1235
X-RAY DIFFRACTION	r_lrange_other	2.452	17.653	1236
X-RAY DIFFRACTION	r_rigid_bond_restr	3.732	3	2217

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
1.42-1.457	0.267	80	0.234	1388	0.235	1955	0.966	0.977	75.0895	0.218
1.457-1.497	0.236	83	0.185	1557	0.188	1894	0.972	0.983	86.5892	0.166
1.497-1.54	0.188	117	0.143	1623	0.146	1842	0.98	0.989	94.4625	0.125
1.54-1.587	0.161	73	0.12	1723	0.121	1806	0.986	0.991	99.4463	0.101
1.587-1.639	0.131	84	0.103	1657	0.104	1741	0.99	0.993	100	0.091
1.639-1.696	0.141	81	0.106	1591	0.108	1672	0.987	0.993	100	0.093
1.696-1.76	0.154	70	0.107	1581	0.108	1651	0.985	0.993	100	0.096
1.76-1.832	0.151	77	0.115	1483	0.116	1560	0.987	0.992	100	0.105
1.832-1.913	0.153	72	0.116	1429	0.118	1501	0.984	0.992	100	0.11
1.913-2.006	0.129	74	0.111	1363	0.112	1437	0.989	0.993	100	0.106
2.006-2.114	0.133	73	0.115	1328	0.116	1401	0.99	0.993	100	0.114
2.114-2.242	0.132	55	0.117	1244	0.117	1299	0.99	0.993	100	0.117
2.242-2.395	0.151	60	0.121	1186	0.122	1246	0.986	0.992	100	0.123
2.395-2.586	0.132	55	0.132	1093	0.132	1148	0.988	0.989	100	0.137
2.586-2.831	0.181	35	0.14	1032	0.141	1067	0.98	0.988	100	0.149
2.831-3.162	0.167	25	0.137	943	0.138	968	0.987	0.988	100	0.149
3.162-3.644	0.13	38	0.134	839	0.134	877	0.992	0.989	100	0.153
3.644-4.447	0.121	27	0.127	717	0.127	744	0.991	0.99	100	0.15
4.447-6.223	0.245	19	0.171	575	0.174	595	0.972	0.986	99.8319	0.217
6.223-30.49	0.163	21	0.217	347	0.213	373	0.981	0.972	98.6595	0.27

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