PDB-6v8h: Crystal structure of Ara h 8.0201

ID or keywords:

Entry

Database: PDB / ID: 6v8h

Title

Crystal structure of Ara h 8.0201

Components

Ara h 8 allergen isoform

Keywords

ALLERGEN / peanut / PR-10

Function / homology

Function and homology information

abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function

Biological species

Arachis hypogaea (peanut)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.31 Å

Authors

Offermann, L.R. / Pote, S. / Hurlburt, B.K. / McBride, J.K. / Chruszcz, M.

Citation

Journal: To Be Published
Title: Crystal structure of Ara h 8.0201
Authors: Offermann, L.R. / Pote, S. / Hurlburt, B.K. / McBride, J.K. / Chruszcz, M.

History

Deposition	Dec 11, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6v8h.cif.gz	464.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6v8h.ent.gz	385.8 KB	Display	PDB format
PDBx/mmJSON format	6v8h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6v8h_validation.pdf.gz	284.5 KB	Display	wwPDB validaton report
Full document	6v8h_full_validation.pdf.gz	284.5 KB	Display
Data in XML	6v8h_validation.xml.gz	1.2 KB	Display
Data in CIF	6v8h_validation.cif.gz	12.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v8/6v8h ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v8h	HTTPS FTP

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Related structure data

Related structure data	6v8jC 6v8lC 6v8mC 6v8sC 4mapS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6v8j-2 6v8l-3 6aww-1 6v8j-3 4cb7-1 6v8l-2 3f59-4 3ia5-1 6akv-d 6v8j-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ara h 8 allergen isoform

C: Ara h 8 allergen isoform

G: Ara h 8 allergen isoform

J: Ara h 8 allergen isoform

L: Ara h 8 allergen isoform

M: Ara h 8 allergen isoform

N: Ara h 8 allergen isoform

O: Ara h 8 allergen isoform

hetero molecules

132 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ara h 8 allergen isoform

defined by author&software
Evidence: gel filtration
16.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Ara h 8 allergen isoform

hetero molecules

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

3

G: Ara h 8 allergen isoform

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

4

J: Ara h 8 allergen isoform

hetero molecules

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

5

L: Ara h 8 allergen isoform

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

6

M: Ara h 8 allergen isoform

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

7

N: Ara h 8 allergen isoform

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

8

O: Ara h 8 allergen isoform

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

Unit cell

Length a, b, c (Å)	65.997, 111.275, 80.021
Angle α, β, γ (deg.)	90.000, 93.700, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 153 / Label seq-ID: 2 - 153

NCS ensembles :

#1: Protein	Ara h 8 allergen isoform Mass: 16432.467 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arachis hypogaea (peanut) / Gene: Ahy_Scaffold6g108211 / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0YIU5
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.25 Å³/Da / Density % sol: 45.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 8 / Details: 0.15M HEPES, 2.4M Ammonium Sulfate, pH 8.0

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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: RAYONIX MX300-HS / Detector: CCD / Date: Jun 28, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→40 Å / Num. obs: 48973 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / R_merge(I) obs: 0.082 / R_pim(I) all: 0.045 / R_rim(I) all: 0.094 / R_sym value: 0.082 / Net I/σ(I): 22.1
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 4 % / R_merge(I) obs: 0.492 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2377 / CC_1/2: 0.84 / CC star: 0.955 / R_pim(I) all: 0.273 / R_rim(I) all: 0.564 / R_sym value: 0.492 / % possible all: 93.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4MAP

4map

Resolution: 2.31→27.83 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.924 / SU B: 22.539 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.284
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2677	2359	4.8 %	RANDOM
R_work	0.2269	-	-	-
obs	0.2289	46590	96.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 171.31 Å² / B_iso mean: 63.81 Å² / B_iso min: 39.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.14 Å²	0 Å²	0.5 Å²
2-	-	0.12 Å²	0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: final / Resolution: 2.31→27.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9076	0	10	240	9326
B_iso mean	-	-	72.98	62.4	-
Num. residues	-	-	-	-	1214

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	9259
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	8670
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.649	12568
X-RAY DIFFRACTION	r_angle_other_deg	1.284	1.582	20278
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.01	5	1205
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.355	26.501	343
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.205	15	1560
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1294
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10239
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1605

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4445	0.06
1	2	C	4445	0.06
2	1	A	4269	0.09
2	2	G	4269	0.09
3	1	A	4416	0.07
3	2	J	4416	0.07
4	1	A	4419	0.07
4	2	L	4419	0.07
5	1	A	4418	0.06
5	2	M	4418	0.06
6	1	A	4410	0.07
6	2	N	4410	0.07
7	1	A	4444	0.06
7	2	O	4444	0.06
8	1	C	4297	0.09
8	2	G	4297	0.09
9	1	C	4474	0.07
9	2	J	4474	0.07
10	1	C	4458	0.07
10	2	L	4458	0.07
11	1	C	4423	0.06
11	2	M	4423	0.06
12	1	C	4385	0.07
12	2	N	4385	0.07
13	1	C	4442	0.06
13	2	O	4442	0.06
14	1	G	4272	0.09
14	2	J	4272	0.09
15	1	G	4316	0.09
15	2	L	4316	0.09
16	1	G	4244	0.09
16	2	M	4244	0.09
17	1	G	4241	0.09
17	2	N	4241	0.09
18	1	G	4268	0.1
18	2	O	4268	0.1
19	1	J	4430	0.07
19	2	L	4430	0.07
20	1	J	4391	0.07
20	2	M	4391	0.07
21	1	J	4357	0.08
21	2	N	4357	0.08
22	1	J	4409	0.07
22	2	O	4409	0.07
23	1	L	4388	0.07
23	2	M	4388	0.07
24	1	L	4376	0.08
24	2	N	4376	0.08
25	1	L	4402	0.08
25	2	O	4402	0.08
26	1	M	4386	0.07
26	2	N	4386	0.07
27	1	M	4406	0.07
27	2	O	4406	0.07
28	1	N	4412	0.07
28	2	O	4412	0.07

LS refinement shell

Resolution: 2.31→2.369 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_free	0.329	161	-
R_work	0.299	3129	-
obs	-	-	88.04 %

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	1.4173	0.3189	-0.0125	4.3877	-0.4965	1.4617	-0.1489	0.0452	0.0822	0.3646	0.0182	-0.4093	0.097	0.0938	0.1306	0.1016	-0.0086	-0.042	0.0136	0.008	0.2736	46.7903	18.0841	57.893
2	0.6466	-1.274	0.342	6.9001	-2.2569	1.9167	-0.0001	0.0712	0.0268	-0.1252	0.016	0.1922	0.1378	-0.102	-0.0159	0.1242	-0.0343	-0.0175	0.0242	0.015	0.2178	38.7237	17.8611	52.5796
3	1.7245	0.0356	0.0373	5.4403	-1.2488	0.3813	-0.0038	0.1211	0.0619	0.2262	0.1926	1.2792	-0.0762	-0.0076	-0.1888	0.152	-0.0861	0.1335	0.0792	0.0168	0.4918	9.209	-7.8768	14.3644
4	2.0841	-1.4894	-0.7643	6.7026	0.748	0.5749	0.0302	-0.0045	-0.1128	0.172	-0.0036	0.5793	0.0085	0.0377	-0.0266	0.1704	-0.1029	0.0985	0.0731	-0.0506	0.2591	17.5301	-8.6595	13.1369
5	2.3781	0.9069	0.5999	6.0962	0.5978	2.7019	-0.1278	0.2675	0.4886	-0.5599	-0.1468	1.009	-0.1697	-0.154	0.2746	0.0901	0.025	-0.1279	0.0609	0.0176	0.3867	12.1262	18.9694	1.158
6	1.1863	2.2738	0.8396	6.7162	1.6999	2.07	-0.0169	0.1272	0.2841	0.0455	-0.0638	0.6009	-0.058	0.1039	0.0807	0.1204	0.0156	-0.0392	0.0615	-0.0014	0.342	19.2924	17.8603	7.5329
7	0.7931	0.0881	0.0834	3.0464	-0.4961	1.0692	-0.0913	0.034	0.0204	0.0926	0.2144	0.6068	0.0451	-0.1339	-0.1231	0.0434	-0.0261	0.0371	0.0469	0.0384	0.4337	6.7483	-8.6206	53.9005
8	1.2045	-0.5366	-0.1035	4.202	0.0826	0.4183	-0.0127	-0.011	-0.0967	0.0749	0.0479	0.2245	0.0221	-0.0488	-0.0351	0.0711	-0.0197	0.0439	0.0118	-0.0123	0.2947	15.1592	-9.2244	53.001
9	2.0466	0.4809	-0.2115	4.8838	-0.9841	1.0701	-0.235	0.0222	0.1943	-0.4298	0.2561	0.7187	-0.0126	-0.077	-0.0211	0.076	-0.0152	-0.1238	0.0167	0.0119	0.3186	8.871	18.9497	41.6616
10	1.3558	1.9679	0.8825	6.2771	1.8058	1.4479	-0.0985	-0.063	0.1693	-0.0551	0.0637	0.318	-0.0023	-0.0456	0.0348	0.0639	0.0241	-0.0589	0.0169	-0.0093	0.3213	16.2683	17.4964	47.6675
11	1.8984	0.1569	-0.3397	7.1278	-1.4256	3.8042	-0.088	-0.0228	-0.107	-0.6095	-0.1368	-0.9339	0.0182	0.309	0.2248	0.0868	-0.012	0.1145	0.0355	-0.0067	0.2124	50.3755	-7.4704	3.0803
12	1.5254	1.501	-0.7817	6.155	-2.6997	2.9653	-0.0229	-0.0425	-0.0783	0.105	0.0589	-0.0712	-0.1789	-0.0079	-0.036	0.148	-0.0123	0.0543	0.0069	-0.0213	0.1939	42.6587	-8.8041	8.7512
13	2.0667	-0.9684	0.2919	5.3932	1.0147	0.9024	-0.1046	0.048	0.0252	-0.1863	0.1245	-0.5941	-0.2032	0.0984	-0.0199	0.0635	-0.0293	0.0319	0.014	-0.0229	0.2988	47.3629	-8.0935	43.5673
14	0.5615	0.4357	-0.4776	6.6192	-0.5645	1.7156	0.0416	-0.0238	-0.088	0.4509	-0.0985	0.244	-0.1707	-0.0974	0.0568	0.1172	-0.0015	0.0478	0.0137	0.0037	0.2245	39.4113	-8.0308	48.6434
15	0.6226	0.4854	-0.3388	6.5598	0.9869	3.6675	-0.1516	-0.0863	0.0422	0.2583	0.5713	-0.8654	0.1269	0.0794	-0.4197	0.0632	0.0576	-0.0321	0.0835	-0.1163	0.3859	50.507	16.5169	17.9793
16	0.6645	-0.1	-0.5198	7.9569	-0.1991	2.3397	-0.102	0.1061	-0.0025	-0.4398	0.3565	0.0211	0.0081	-0.1842	-0.2545	0.0809	-0.0569	-0.0108	0.0539	0.0227	0.163	42.7368	18.0451	14.2703

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 92
2	X-RAY DIFFRACTION	2	A	93 - 153
3	X-RAY DIFFRACTION	3	C	2 - 67
4	X-RAY DIFFRACTION	4	C	68 - 153
5	X-RAY DIFFRACTION	5	G	2 - 86
6	X-RAY DIFFRACTION	6	G	87 - 153
7	X-RAY DIFFRACTION	7	J	2 - 67
8	X-RAY DIFFRACTION	8	J	68 - 153
9	X-RAY DIFFRACTION	9	L	2 - 90
10	X-RAY DIFFRACTION	10	L	91 - 153
11	X-RAY DIFFRACTION	11	M	2 - 85
12	X-RAY DIFFRACTION	12	M	86 - 153
13	X-RAY DIFFRACTION	13	N	2 - 92
14	X-RAY DIFFRACTION	14	N	93 - 153
15	X-RAY DIFFRACTION	15	O	2 - 73
16	X-RAY DIFFRACTION	16	O	74 - 153

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