PDB-3f5v: C2 Crystal form of mite allergen DER P 1

ID or keywords:

Entry

Database: PDB / ID: 3f5v

Title

C2 Crystal form of mite allergen DER P 1

Components

Der p 1 allergen

Keywords

HYDROLASE / ALLERGY /

ASTHMA /

DUST MITES /

ALLERGEN /

GLYCOPROTEIN /

PROTEASE /

SECRETED /

THIOL PROTEASE

Function / homology

Function and homology information

cysteine-type peptidase activity /

proteolysis /

metal ion binding
Similarity search - Function

Biological species

Dermatophagoides pteronyssinus (European house dust mite)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.36 Å

Authors

Stura, E.A. / Minor, W. / Chruszcz, M. / Saint Remy, J.M.

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of mite allergens Der f 1 and Der p 1 reveal differences in surface-exposed residues that may influence antibody binding.
Authors: Chruszcz, M. / Chapman, M.D. / Vailes, L.D. / Stura, E.A. / Saint-Remy, J.M. / Minor, W. / Pomes, A.

History

Deposition	Nov 4, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3f5v.cif.gz	122.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3f5v.ent.gz	95 KB	Display	PDB format
PDBx/mmJSON format	3f5v.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5v ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5v	HTTPS FTP

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Related structure data

Related structure data	5vpkC 2as8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3mms-d 5wi7-2 3lq0-d 1im8-2 4jlv-d 1xi6-d 3eis-1 5lqj-4 6n6y-d 2vyo-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#142 - Oct 2011 PDB Pioneers similarity (12)

Deposited unit

A: Der p 1 allergen

B: Der p 1 allergen

hetero molecules

51.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Der p 1 allergen

hetero molecules

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

2

B: Der p 1 allergen

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.196, 84.070, 75.437
Angle α, β, γ (deg.)	90.00, 123.81, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Der p 1 allergen Mass: 25060.830 Da / Num. of mol.: 2 / Mutation: N52Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite) Gene: DERP1 / Plasmid: PCR4-BLUNT / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: Q3HWZ5, peptidase 1 (mite)
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 679 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.84 %
Crystal grow	pH: 5.75 Details: 3.5MG/ML DER P1 NON GLYCOSYLATED IN 50MM NA ACETATE, 0.005% AZ, LOW SALT, PH 5.75, SLOW EVAPORATION, TEMPERATURE 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 / Wavelength: 1.0723 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2006 / Details: MIRRORS
Radiation	Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0723 Å / Relative weight: 1
Reflection	Resolution: 1.36→50 Å / Num. obs: 103499 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 12.6 Å² / R_merge(I) obs: 0.069 / R_sym value: 0.069 / Net I/σ(I): 25.3
Reflection shell	Resolution: 1.36→1.38 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.551 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4795 / R_sym value: 0.551 / % possible all: 91.5

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Processing

Software

Name	Version	Classification
MOLREP		phasing
Coot		model building
REFMAC	5.5.0062	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2AS8

2as8

Resolution: 1.36→35.81 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.953 / SU B: 1.657 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.051 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18338	5200	5 %	RANDOM
R_work	0.15761	-	-	-
all	0.1589	98812	-	-
obs	0.1589	98812	98.4 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 8.867 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.2 Å²	0 Å²	0.16 Å²
2-	-	-0.06 Å²	0 Å²
3-	-	-	0.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.36→35.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3524	0	40	679	4243

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	3838
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2556
X-RAY DIFFRACTION	r_angle_refined_deg	1.732	1.923	5239
X-RAY DIFFRACTION	r_angle_other_deg	2.332	3.004	6149
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.834	5	481
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.214	23.732	209
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.145	15	576
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.505	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.311	0.2	534
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4500
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	841
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.059	1.5	2319
X-RAY DIFFRACTION	r_mcbond_other	0.159	1.5	946
X-RAY DIFFRACTION	r_mcangle_it	1.815	2	3750
X-RAY DIFFRACTION	r_scbond_it	2.831	3	1519
X-RAY DIFFRACTION	r_scangle_it	4.428	4.5	1489
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.36→1.395 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.267	369	-
R_work	0.273	6818	-
obs	-	-	92.2 %

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	0.5002	-0.4353	-0.3429	7.3949	-1.0418	1.2044	-0.0947	0.1451	0.0156	-0.6922	0.003	-0.0048	0.1847	-0.1459	0.0917	0.1186	-0.0338	-0.0376	0.0783	-0.0123	0.0768	36.6145	-18.788	-37.8038
2	4.5564	0.6148	0.0472	3.1929	-0.5335	1.7857	-0.0061	0.156	-0.3182	-0.1342	-0.0381	-0.3005	0.3388	0.0943	0.0442	0.0649	0.0184	0.0089	0.0143	-0.0163	0.0871	51.0187	-25.2441	-27.4738
3	0.7965	0.2557	0.0331	0.8242	-0.0715	0.8158	-0.015	0.0681	0.0346	-0.0565	-0.0084	-0.0444	-0.025	0.0195	0.0233	0.013	0.0026	0.0083	0.0134	0.0034	0.0124	52.0761	-4.0892	-30.1101
4	0.4998	-0.1757	-0.6914	4.1735	0.29	1.6935	0.059	0.0135	0.0332	0.2093	-0.0802	-0.2357	-0.4504	0.1546	0.0212	0.2167	-0.0586	-0.024	0.1193	0.0064	0.1623	56.1543	8.4968	-25.2864
5	2.7273	1.4231	-0.5343	1.3775	-0.1144	0.7432	0.0037	0.2095	0.0732	-0.1428	0.0456	0.0857	-0.0583	-0.0715	-0.0493	0.0341	0.0144	-0.011	0.0368	0.0149	0.0245	46.9851	-4.6407	-37.5472
6	1.3954	-0.1093	0.0548	1.3114	0.161	1.0772	-0.0466	-0.2048	-0.0651	0.1041	0.033	0.1044	0.0957	-0.0894	0.0136	0.0221	0.0016	0.0192	0.0404	0.0068	0.029	39.9915	-16.6147	-19.1773
7	1.8222	-0.4114	-0.9546	0.6839	-0.0625	1.1859	0.0084	-0.1826	0.0123	0.0381	0.0604	-0.062	-0.012	-0.0324	-0.0688	0.0345	0.005	-0.0121	0.0654	0.0041	0.0277	38.2796	-13.4737	-18.4648
8	1.2774	0.0741	-0.1018	1.3797	-0.0501	0.7382	-0.003	-0.1125	-0.0818	0.0888	0.0051	0.0449	0.0554	-0.0567	-0.0021	0.0142	-0.004	0.0096	0.0165	0.0071	0.0229	42.3417	-16.1998	-21.4528
9	0.3323	0.0686	-0.0516	4.9893	-0.1453	0.5203	0.0487	0.0685	-0.0061	0.0779	0.048	0.3224	-0.0606	-0.168	-0.0967	0.0296	0.0224	-0.0115	0.0708	0.0234	0.0868	15.9751	20.1382	-5.0434
10	2.8238	0.5862	-0.3189	3.8136	-0.2335	3.9667	0.053	-0.1339	0.1895	0.2964	-0.057	-0.047	-0.1712	-0.1059	0.0039	0.0515	0.0076	-0.0094	0.0131	-0.0124	0.0349	29.3466	24.2756	4.9576
11	0.6181	-0.1101	0.0555	0.7885	-0.3584	0.719	0.0007	-0.0203	-0.0149	0.0482	-0.001	0.0085	0.0122	-0.0528	0.0004	0.0075	-0.0048	0.0056	0.0073	-0.0031	0.0111	27.8354	3.9356	6.4137
12	2.0616	-1.7272	-1.7393	2.0992	1.9277	2.6743	-0.0325	-0.042	-0.0955	0.1243	0.0272	0.0307	0.1314	-0.0852	0.0053	0.0288	-0.0065	0.0002	0.0163	0.0072	0.0209	29.314	-6.8164	12.4897
13	0.4996	0.0167	-0.1649	0.9248	-0.1703	1.3732	0.021	0.025	0.0174	-0.0996	0.023	0.079	-0.0403	-0.061	-0.044	0.0155	0.0049	-0.0113	0.0179	-0.0038	0.023	22.9332	13.1163	-5.5649
14	0.2561	-0.9473	0.2498	4.6591	0.4616	3.826	0.0535	0.0921	0.1275	-0.1817	0.0443	-0.4733	-0.0079	0.4471	-0.0978	0.0226	0.0065	0.05	0.1716	0.0388	0.1243	42.5583	16.8967	-10.8519
15	0.8555	0.1891	-0.5165	0.9818	0.7126	2.2733	-0.0114	0.0999	0.0655	-0.1029	0.0373	-0.0461	-0.097	0.0845	-0.0259	0.0136	-0.0025	0.0054	0.0277	0.0142	0.0242	32.4907	16.8732	-10.2788
16	0.6768	-0.1544	-0.0161	1.3802	-0.0191	0.7516	0.0149	0.0431	0.0392	-0.0896	-0.021	-0.0976	-0.0159	0.0167	0.0061	0.0066	0.0006	0.0052	0.0043	0.0054	0.0121	31.8401	14.3332	-5.3566

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 12
2	X-RAY DIFFRACTION	2	A	13 - 20
3	X-RAY DIFFRACTION	3	A	21 - 97
4	X-RAY DIFFRACTION	4	A	98 - 104
5	X-RAY DIFFRACTION	5	A	105 - 122
6	X-RAY DIFFRACTION	6	A	123 - 163
7	X-RAY DIFFRACTION	7	A	164 - 181
8	X-RAY DIFFRACTION	8	A	182 - 222
9	X-RAY DIFFRACTION	9	B	1 - 13
10	X-RAY DIFFRACTION	10	B	14 - 20
11	X-RAY DIFFRACTION	11	B	21 - 98
12	X-RAY DIFFRACTION	12	B	99 - 109
13	X-RAY DIFFRACTION	13	B	110 - 149
14	X-RAY DIFFRACTION	14	B	150 - 163
15	X-RAY DIFFRACTION	15	B	164 - 187
16	X-RAY DIFFRACTION	16	B	188 - 222

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