PDB-4aud: Crystal structure of alternaria alternata major allergen alt a 1

ID or keywords:

Entry

Database: PDB / ID: 4aud

Title

Crystal structure of alternaria alternata major allergen alt a 1

Components

MAJOR ALLERGEN ALT A 1 SUBUNIT

Keywords

ALLERGEN / MAJOR ALLERGEN NEST /

ANION BINDING

Function / homology

Function and homology information

ascospore wall / extracellular region
Similarity search - Function

Biological species

ALTERNARIA ALTERNATA (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.67 Å

Authors

Mechaly, A.E. / Ibanez de Opakua, A. / Asturias, J. / Viguera, A.R.

Citation

Journal: To be Published
Title: Crystal Structure of Major Allergen of Alternaria Alternata Alt a 1
Authors: Mechaly, A.E. / Ibanez De Opakua, A. / Bermejo, I. / Asturias, J. / Viguera, A.R.

History

Deposition	May 16, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 29, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4aud.cif.gz	106.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4aud.ent.gz	90.1 KB	Display	PDB format
PDBx/mmJSON format	4aud.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/au/4aud ftp://data.pdbj.org/pub/pdb/validation_reports/au/4aud	HTTPS FTP

-
Related structure data

Similar structure data	7km6-d 6chl-1 5nja-2 1vlh-d 5nj9-2 5njc-1 5njf-2 6b7a-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MAJOR ALLERGEN ALT A 1 SUBUNIT

B: MAJOR ALLERGEN ALT A 1 SUBUNIT

hetero molecules

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

1

A: MAJOR ALLERGEN ALT A 1 SUBUNIT

B: MAJOR ALLERGEN ALT A 1 SUBUNIT

hetero molecules

A: MAJOR ALLERGEN ALT A 1 SUBUNIT

B: MAJOR ALLERGEN ALT A 1 SUBUNIT

hetero molecules

A: MAJOR ALLERGEN ALT A 1 SUBUNIT

B: MAJOR ALLERGEN ALT A 1 SUBUNIT

hetero molecules

defined by author&software
87.1 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.370, 141.370, 141.370
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	212
Space group name H-M	P4₃32

#1: Protein	MAJOR ALLERGEN ALT A 1 SUBUNIT Mass: 14417.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-157 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ALTERNARIA ALTERNATA (fungus) / Plasmid: PKN172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834 / References: UniProt: Q6Q128, UniProt: P79085*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, LEU 81 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 81 TO MET

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.08 Å³/Da / Density % sol: 65 % / Description: NONE
Crystal grow	pH: 7.4 Details: 4M SODIUM SULFATE, 100MM HEPES, 50MM CADMIUM SULFATE, PH 7.4

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2010
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.67→63.23 Å / Num. obs: 14251 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / B_iso Wilson estimate: 57.31 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shell	Resolution: 2.67→2.81 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
SHELX		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.67→99.964 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 22.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2403	694	5 %
R_work	0.1953	-	-
obs	0.1974	13832	96.89 %

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.655 Å² / k_sol: 0.347 e/Å³

Displacement parameters

B_iso mean: 62.21 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2.67→99.964 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1906	0	10	45	1961

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1964
X-RAY DIFFRACTION	f_angle_d	1.199	2652
X-RAY DIFFRACTION	f_dihedral_angle_d	14.413	690
X-RAY DIFFRACTION	f_chiral_restr	0.072	276
X-RAY DIFFRACTION	f_plane_restr	0.004	342

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6702-2.8764	0.4016	141	0.3297	2354	X-RAY DIFFRACTION	90
2.8764-3.1659	0.3016	135	0.2437	2535	X-RAY DIFFRACTION	96
3.1659-3.624	0.2541	140	0.204	2639	X-RAY DIFFRACTION	98
3.624-4.5659	0.2162	151	0.1634	2697	X-RAY DIFFRACTION	100
4.5659-100.0338	0.1959	127	0.1797	2913	X-RAY DIFFRACTION	100

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	3.1357	1.108	1.7024	0.4032	0.6476	1.0295	-0.873	0.3517	0.8649	0.5192	1.5999	0.98	-0.3183	0.7726	0.3368	0.4818	0.0546	0.1211	0.3604	0.045	0.4935	65.3217	77.4556	57.4603
2	0.6	0.4392	0.2119	0.596	-0.1941	0.1378	0.0202	0.4954	-0.3189	0.0489	-0.417	0.4155	0.0117	-0.0766	0.0003	0.3778	0.0821	-0.0183	0.3988	0.0288	0.3751	70.2901	65.3518	47.3817
3	0.6803	-0.5969	0.1956	0.8654	0.1361	0.3359	0.0225	0.1373	0.4487	-1.0577	0.1204	-0.3245	-0.5395	-0.5808	0.0228	0.3533	0.0099	0.0084	0.383	0.0771	0.3637	77.8142	70.1979	40.8683
4	0.1009	0.0829	0.2386	0.2596	0.3433	0.2456	0.1255	-0.0751	0.2415	0.0302	-0.1199	-0.4723	-0.0452	0.3761	0.0001	0.3429	0.0138	0.0266	0.4033	0.092	0.481	76.1374	76.6898	49.1564
5	1.0734	-0.7754	-0.1613	0.4487	0.2049	0.1408	-0.0451	0.0115	-0.0009	0.1197	-0.0091	0.0906	0.1913	-0.0417	0.0003	0.3949	-0.0015	0.0397	0.3512	0.0099	0.2648	74.0684	64.0505	52.0317
6	0.0686	0.0002	0.2126	0.0151	0.0041	0.3838	-0.6721	0.1008	-0.2614	-0.1171	0.6408	0.2814	0.7619	1.4346	0.0152	0.4804	0.1644	-0.0189	0.5568	0.0819	0.5215	86.5217	73.9543	66.7253
7	0.7158	0.203	-0.3235	0.1802	0.2569	0.8207	0.018	0.0645	0.482	0.3763	-0.0717	0.1164	-0.3709	0.2304	-0	0.3255	-0.0341	-0.0283	0.415	-0.048	0.5357	84.7302	90.8761	68.1839
8	0.0972	-0.0477	-0.0631	0.0619	0.0187	0.068	0.2451	-0.8257	-0.5816	0.5036	-0.5785	-0.1093	0.704	0.0516	-0.0007	0.5667	-0.2058	-0.1103	0.6836	0.0179	0.6458	91.455	89.5791	66.2623
9	0.2959	-0.0059	0.1447	0.2398	0.329	0.6646	0.12	0.1711	-0.0311	-0.905	0.0534	-0.2766	-1.0284	1.4923	-0.0432	0.4966	-0.2575	-0.0125	0.5657	0.119	0.6495	87.4304	93.9204	57.4921
10	1.3753	0.5793	-0.9873	0.9245	0.8211	3.2467	0.5039	-0.2697	-0.214	-0.9611	0.2429	0.9025	-0.8453	0.5364	0.4409	0.3579	-0.0484	-0.04	0.5664	0.0597	0.7347	80.0271	89.1166	60.1502
11	0.2616	0.2518	0.2291	0.2155	0.1316	0.2194	0.54	-0.3013	0.1227	-0.4167	-0.2728	-0.1813	-0.3405	0.3754	0.0004	0.477	0.0349	0.0049	0.5902	-0.025	0.6057	87.9706	80.0115	55.3865
12	0.9102	0.7849	0.6023	1.9196	0.1819	0.5523	-0.0021	-0.0007	0.2005	0.1276	-0.0402	1.0292	-0.2882	0.0874	0.5997	0.5743	-0.2018	-0.0339	0.3416	-0.0492	0.5108	79.987	89.6083	67.6573

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 7:16)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 17:50)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 51:67)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 68:96)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 97:129)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 7:16)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 17:43)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 44:50)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 51:67)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 68:77)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 78:96)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 97:129)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi