PDB-1pyu: Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys

ID or keywords:

Entry

Database: PDB / ID: 1pyu

Title

Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys

Components

Aspartate 1-decarboxylase alfa chain
Aspartate 1-decarboxylase beta chain

Keywords

LYASE / Auto-processing / Aspartate Decarboxylase / pyruvoyl

Function / homology

Function and homology information

alanine biosynthetic process /

aspartate 1-decarboxylase /

aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing /

cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Schmitzberger, F. / Kilkenny, M.L. / Lobley, C.M.C. / Webb, M.E. / Vinkovic, M. / Matak-Vinkovic, D. / Witty, M. / Chirgadze, D.Y. / Smith, A.G. / Abell, C. / Blundell, T.L.

Citation

Journal: Embo J. / Year: 2003
Title: Structural Constraints on protein self-processing in L-aspartate-alpha-decarboxylase
Authors: Schmitzberger, F. / Kilkenny, M.L. / Lobley, C.M.C. / Webb, M.E. / Vinkovic, M. / Matak-Vinkovic, D. / Witty, M. / Chirgadze, D.Y. / Smith, A.G. / Abell, C. / Blundell, T.L.

History

Deposition	Jul 9, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Oct 27, 2021	Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 16, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Remark 999

SEQUENCE The author states that this particulr protein self-processes in order to become ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1pyu.cif.gz	111.2 KB	Display	PDBx/mmCIF format
PDB format	pdb1pyu.ent.gz	87.9 KB	Display	PDB format
PDBx/mmJSON format	1pyu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/py/1pyu ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyu	HTTPS FTP

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Related structure data

Related structure data	1ppyC 1pqeC 1pqfC 1pqhC 1pt0C 1pt1C 1pyqC 1aw8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1pt0-1 4azd-1 1pqh-1 4aok-1 1pyq-1 1pt1-1 1ppy-1 2wd5-d 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	#80 - Aug 2006 AAA+ Proteases similarity (1) #144 - Dec 2011 Complex I similarity (1) #167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alfa chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alfa chain

hetero molecules

31.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alfa chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alfa chain

hetero molecules

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alfa chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alfa chain

hetero molecules

defined by author&software
63.6 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.787, 70.787, 217.121
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Details

The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the symmetry operation x, x-y, 1/6-z.

#1: Protein/peptide	Aspartate 1-decarboxylase beta chain / Aspartate alpha-decarboxylase Mass: 4770.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAND / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Protein	Aspartate 1-decarboxylase alfa chain / Aspartate alpha-decarboxylase Mass: 11043.412 Da / Num. of mol.: 2 / Mutation: S25C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAND / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 180 / 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: 50.3 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M citric acid, 1.6M ammonium sulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal grow

*PLUS

Temperature: 19 ℃ / pH: 4 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	5-9 mg/ml	protein	1	drop
2	1.4-1.6 M	ammonium sulfate	1	reservoir
3	0.1 M	citric acid	1	reservoir	pH4.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2003 / Details: Osmic Confocal MaxFlux optic system
Radiation	Monochromator: osmium mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. all: 26051 / Num. obs: 25322 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.6 % / B_iso Wilson estimate: 31.7 Å² / R_sym value: 0.082 / Net I/σ(I): 28.3
Reflection shell	Resolution: 1.9→1.92 Å / Mean I/σ(I) obs: 3.011 / Num. unique all: 767 / R_sym value: 0.323 / % possible all: 88.3
Reflection	PLUS Lowest resolution: 30 Å / Num. obs: 26469 / % possible obs: 98.9 % / Redundancy: 29.8 % / R_merge(I) obs*: 0.082
Reflection shell	PLUS % possible obs: 88.3 % / R_merge(I) obs: 0.323 / Mean I/σ(I) obs*: 3

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1aw8

1aw8

Resolution: 1.9→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.956 / SU B: 2.29 / SU ML: 0.067 / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19614	1325	5.1 %	RANDOM
R_work	0.17256	-	-	-
obs	0.17379	24733	98.62 %	-
all	-	26051	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.54 Å²	0.27 Å²	0 Å²
2-	-	0.54 Å²	0 Å²
3-	-	-	-0.81 Å²

Refine analyze

Luzzati coordinate error obs: 0.213 Å

Refinement step

Cycle: LAST / Resolution: 1.9→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1777	0	10	180	1967

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	1828
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	1654
X-RAY DIFFRACTION	r_angle_refined_deg	1.417	1.924	2473
X-RAY DIFFRACTION	r_angle_other_deg	1.153	3	3817
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.168	5	231
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	280
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2061
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	381
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	300
X-RAY DIFFRACTION	r_nbd_other	0.253	0.2	1919
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	1140
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.27	0.2	126
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.199	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.341	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.272	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	0.636	1.5	1160
X-RAY DIFFRACTION	r_mcangle_it	1.148	2	1844
X-RAY DIFFRACTION	r_scbond_it	1.921	3	668
X-RAY DIFFRACTION	r_scangle_it	3.029	4.5	629

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.267	-
R_work	0.234	1641

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	28.2615	-4.1519	17.3583	24.7377	9.1419	12.8485	0.7885	-0.3773	-1.4861	-0.5293	-0.5419	2.4216	1.1772	-1.6558	-0.2466	0.2279	-0.1135	-0.0615	0.2839	-0.0321	0.3621	41.1139	29.5785	11.6082
2	3.3154	1.2993	3.0026	1.7149	2.5352	4.2495	-0.2697	-0.0477	0.4921	-0.1892	0.039	0.1791	-0.4449	0.1341	0.2307	0.1062	-0.017	-0.0131	0.0631	-0.0107	0.0976	53.5679	46.8158	26.6438
3	-12.9832	-24.1698	-41.4979	73.0078	25.007	67.8794	-0.6709	-1.9524	0.3411	3.037	1.8727	-3.2573	2.54	3.2721	-1.2018	0.2501	0.0398	-0.1951	0.3921	-0.1258	0.2933	67.8625	44.575	39.7651
4	80.5465	51.5324	-20.9997	80.5669	-31.1731	27.7975	1.2925	-0.9788	-2.8341	2.7809	-0.9975	-0.172	0.7836	0.7718	-0.2949	0.5385	0.1086	-0.1114	0.5618	-0.1053	0.4593	69.7464	35.5585	39.8863
5	33.1149	2.5782	-6.107	30.4529	14.0079	40.0215	0.3551	0.1928	-0.461	0.0005	0.1261	-1.8306	2.7625	0.1109	-0.4812	0.2969	-0.0491	-0.0911	0.1984	0.0112	0.233	60.9442	39.3743	35.9897
6	-9.0581	13.0255	26.9118	3.9465	11.8502	-10.3367	0.0338	0.0396	0.0221	0.6092	-0.1904	-0.0995	-0.0667	0.2718	0.1566	0.1758	-0.0157	-0.0012	0.1779	-0.0079	0.0333	55.1618	43.7951	38.1029
7	11.6202	4.7989	9.2232	9.5288	3.877	14.8688	0.2951	-0.6392	-0.3028	0.5651	-0.1585	0.265	0.0957	-0.3925	-0.1367	0.1259	-0.0231	-0.0108	0.1421	-0.03	0.0598	49.6184	44.2523	37.2066
8	1.4459	0.6701	0.729	3.1248	1.3122	0.9736	-0.0456	-0.2077	-0.0131	0.1642	-0.0077	-0.0712	0.0283	0.1009	0.0534	0.0781	-0.0071	-0.0249	0.1209	-0.0078	0.0673	58.1693	42.4788	32.0945
9	50.9469	-30.3	-4.8562	34.2411	12.1018	26.7308	-0.0551	0.2617	-0.7388	0.2605	0.6283	-0.4114	1.4064	0.4854	-0.5732	0.1713	-0.0637	-0.0598	0.1114	-0.0762	0.1314	63.0937	43.6263	36.5076
10	19.1423	1.2314	-6.0327	45.0131	-7.554	-8.236	-0.6384	-0.1526	-0.6354	1.1496	0.5088	-0.3891	-0.4902	-0.0172	0.1296	0.219	0.0527	-0.0879	0.2371	-0.078	0.1389	70.8262	39.8242	32.2879
11	2.7192	2.4808	3.2796	2.6257	3.0891	4.8212	-0.109	-0.2878	0.3441	-0.1081	-0.2152	0.3068	-0.2688	-0.4323	0.3241	0.1217	0.0005	-0.028	0.1272	-0.0191	0.0997	50.337	46.9013	26.7822
12	3.5629	2.4411	0.0604	8.2533	0.2934	2.336	-0.2144	0.2687	0.1337	-0.7453	0.0648	-0.4584	-0.1234	0.0586	0.1497	0.0686	0.0004	-0.0136	0.1044	0.0195	0.0538	55.4099	39.12	5.5439
13	8.9798	6.4925	-18.7699	-3.4731	1.4647	50.4114	0.2891	-1.6298	0.912	0.0578	-0.1772	-0.1559	-3.0164	2.9967	-0.1119	0.575	-0.0219	-0.0881	0.4966	-0.0214	0.6355	59.0083	58.7457	18.8702
14	36.9622	-9.9642	20.3432	74.6461	-24.9846	-32.022	0.1001	-0.6359	-1.1985	2.7163	0.2923	0.7281	-1.6559	-0.0524	-0.3924	0.3133	0.0067	0.0897	0.2234	0.036	0.3856	54.181	51.8386	14.4354
15	15.391	3.0305	-6.553	1.5454	19.711	-4.6522	-0.3187	-0.0658	0.1015	0.1182	0.325	0.7711	0.2396	0.0016	-0.0063	0.2486	0.0093	0.0332	0.0542	0.1082	0.3167	50.818	52.3193	7.6514
16	6.4944	0.3111	1.3748	23.6278	3.7641	8.1044	-0.1049	0.5246	1.1309	0.1227	-0.223	0.7577	-0.4489	-0.2125	0.3279	0.1871	0.0201	-0.0272	0.1161	0.125	0.2539	47.2224	49.3401	4.4511
17	6.3606	0.9782	-1.1928	1.0171	0.1358	2.731	0.0422	0.1298	0.7662	-0.1975	0.0314	0.0136	-0.4274	-0.016	-0.0736	0.1782	-0.0166	-0.0095	0.0666	0.0191	0.1592	55.2821	48.2336	10.3176
18	19.4673	-8.6035	14.1807	21.858	-4.2164	13.6704	-0.1377	-1.0063	0.3484	1.2906	0.8569	-0.1033	-0.0502	-0.2752	-0.7192	0.3215	-0.0169	0.0488	0.1783	0.0915	0.3243	57.3915	54.2093	11.8317
19	21.6467	6.8252	-6.6062	3.1102	6.4204	31.5372	1.1484	-0.1885	0.7084	-0.1931	-0.6042	0.093	-0.5593	-0.8149	-0.5442	0.376	-0.0809	0.0117	0.1338	0.0253	0.2174	63.3926	52.8698	19.1722
20	3.8286	3.843	0.4791	7.6002	0.6063	1.7164	-0.2252	0.5491	0.3298	-0.7006	0.2506	0.1624	-0.3439	0.0459	-0.0254	0.1643	0.0131	0.003	0.1702	0.05	0.1092	54.1656	40.9624	3.046

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-3 - 2	14 - 19
2	X-RAY DIFFRACTION	2	A	A	3 - 16	20 - 33
3	X-RAY DIFFRACTION	3	A	A	17 - 19	34 - 36
4	X-RAY DIFFRACTION	4	A	A	20 - 24	37 - 41
5	X-RAY DIFFRACTION	5	B	B	25 - 27	1 - 3
6	X-RAY DIFFRACTION	6	B	B	28 - 29	4 - 5
7	X-RAY DIFFRACTION	7	B	B	30 - 36	6 - 12
8	X-RAY DIFFRACTION	8	B	B	37 - 68	13 - 44
9	X-RAY DIFFRACTION	9	B	B	69 - 72	45 - 48
10	X-RAY DIFFRACTION	10	B	B	73 - 77	49 - 53
11	X-RAY DIFFRACTION	11	B	B	78 - 116	54 - 92
12	X-RAY DIFFRACTION	12	C	C	1 - 16	18 - 33
13	X-RAY DIFFRACTION	13	C	C	17 - 24	34 - 41
14	X-RAY DIFFRACTION	14	D	D	25 - 27	1 - 3
15	X-RAY DIFFRACTION	15	D	D	28 - 29	4 - 5
16	X-RAY DIFFRACTION	16	D	D	30 - 36	6 - 12
17	X-RAY DIFFRACTION	17	D	D	37 - 68	13 - 44
18	X-RAY DIFFRACTION	18	D	D	69 - 72	45 - 48
19	X-RAY DIFFRACTION	19	D	D	73 - 77	49 - 53
20	X-RAY DIFFRACTION	20	D	D	78 - 115	54 - 91

Refinement

*PLUS

Num. reflection obs: 24377 / R_factor R_free: 0.195 / R_factor R_work: 0.174

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.016
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.56

LS refinement shell

*PLUS

R_factor R_free: 0.268 / R_factor R_work: 0.232

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