PDB-1pqe: S25A mutant of pyruvoyl dependent aspartate decarboxylase

ID or keywords:

Entry

Database: PDB / ID: 1pqe

Title

S25A mutant of pyruvoyl dependent aspartate decarboxylase

Components

Aspartate 1-decarboxylase

Keywords

LYASE / pyruvoyl-dependent enzyme / intramolecular self-processing

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: 1.95 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	Jun 18, 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 / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Aug 16, 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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Download

PDBx/mmCIF format	1pqe.cif.gz	64.8 KB	Display	PDBx/mmCIF format
PDB format	pdb1pqe.ent.gz	49.3 KB	Display	PDB format
PDBx/mmJSON format	1pqe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1pqe_validation.pdf.gz	418.9 KB	Display	wwPDB validaton report
Full document	1pqe_full_validation.pdf.gz	419.1 KB	Display
Data in XML	1pqe_validation.xml.gz	8.2 KB	Display
Data in CIF	1pqe_validation.cif.gz	11.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pq/1pqe ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pqe	HTTPS FTP

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Related structure data

Related structure data	1ppyC 1pqfC 1pqhC 1pt0C 1pt1C 1pyqC 1pyuC 1aw8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4aok-1 6oz8-1 1pyq-1 1aw8-1 4aon-1 1pqf-1 6oz8-2 1pt0-1 4azd-1 1ppy-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

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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

13.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate 1-decarboxylase

defined by author&software
55.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.056, 73.056, 111.114
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-242- HOH

Details

The asymmetric unit contains one protomer. The biological unit is a tetramer which is created by applying the following symmetry operations: 1-x,1-y,z; 1-y,x,z; y,1-x,z.

#1: Protein	Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase Mass: 13834.715 Da / Num. of mol.: 1 / Mutation: S25A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAND / Plasmid: pDKS1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-B / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase

Mass: 13834.715 Da / Num. of mol.: 1 / Mutation: S25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: PAND / Plasmid: pDKS1 / Production host:

Escherichia coli (E. coli) / Strain (production host): XL1-B / References: UniProt: P0A790, aspartate 1-decarboxylase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.9 Å³/Da / Density % sol: 57.9 %

Crystal grow

Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: NH42SO4,Tris/HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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	1.5 M	ammonium sulfate	1	reservoir
3	0.15 M	Tris-HCl	1	reservoir	pH8.0

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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: Sep 7, 1999 / Details: mirrors
Radiation	Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.95→30 Å / Num. obs: 11321 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 9.3 % / B_iso Wilson estimate: 26.7 Å² / R_sym value: 0.04 / Net I/σ(I): 36.6
Reflection shell	Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 4.2 / R_sym value: 0.328 / % possible all: 92.7
Reflection	PLUS Lowest resolution: 25 Å / R_merge(I) obs*: 0.04
Reflection shell	PLUS % possible obs: 92.7 % / R_merge(I) obs*: 0.328

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1aw8

1aw8

Resolution: 1.95→24.5 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.943 / SU B: 2.835 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20492	518	4.8 %	RANDOM
R_work	0.15804	-	-	-
all	0.16032	11321	-	-
obs	0.16032	10244	95.13 %	-

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: 7.708 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	0 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	-0.45 Å²

Refine analyze

Luzzati coordinate error free: 0.132 Å

Refinement step

Cycle: LAST / Resolution: 1.95→24.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	894	0	0	144	1038

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	915
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	833
X-RAY DIFFRACTION	r_angle_refined_deg	1.486	1.911	1240
X-RAY DIFFRACTION	r_angle_other_deg	0.789	3	1917
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.752	5	116
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	140
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1042
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	196
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	170
X-RAY DIFFRACTION	r_nbd_other	0.262	0.2	951
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	549
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	82
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.143	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.32	0.2	62
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.181	0.2	33
X-RAY DIFFRACTION	r_mcbond_it	0.602	1.5	579
X-RAY DIFFRACTION	r_mcangle_it	0.904	2	923
X-RAY DIFFRACTION	r_scbond_it	1.632	3	336
X-RAY DIFFRACTION	r_scangle_it	2.205	4.5	317

LS refinement shell

Resolution: 1.952→2.003 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.189	33
R_work	0.173	729

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	3.9255	-0.5428	-2.4846	1.7447	-0.3091	5.0719	0.042	0.0801	0.2774	-0.1089	0.1593	-0.0148	-0.2403	-0.1782	-0.2013	0.1143	0.01	-0.0289	0.0908	0.038	0.1011	27.1484	47.1412	36.2593
2	11.247	93.6696	-56.8062	-42.5016	58.4745	4.6784	3.1292	-1.7623	-2.8614	-0.8852	-1.853	1.6337	1.049	0.6267	-1.2762	0.2602	-0.0062	0.0113	0.3259	0.0312	0.3293	17.8142	32.0806	50.4655
3	4.6943	9.7652	-4.1244	68.6635	-45.2468	32.824	-0.2504	-0.1547	-1.0494	-1.6809	1.6156	1.7437	2.577	-2.5952	-1.3653	0.4273	-0.2026	-0.049	0.399	0.108	0.539	16.3775	30.5839	43.9874
4	6.6769	-29.9843	12.0287	50.2479	-15.1204	4.3408	-0.0199	-0.3446	-0.6617	-0.216	0.9058	1.1473	-0.1343	-0.6107	-0.8859	0.0762	0.0137	-0.0454	0.1869	0.0356	0.1561	15.2632	42.385	38.1837
5	11.9641	0.294	-8.9756	2.2208	-4.3737	14.3064	0.0635	0.118	0.1254	-0.4941	0.1137	0.3061	0.1416	-0.2682	-0.1772	0.1389	0.0875	-0.0457	0.1718	0.0712	0.1618	15.5718	46.8234	33.0139
6	11.521	-0.1878	-1.0082	22.1702	2.3585	1.8953	0.3226	0.4743	0.0613	-0.4255	-0.2107	0.1611	-0.0221	-0.6629	-0.1118	0.1079	0.0346	-0.0389	0.2363	0.0916	0.0622	20.8983	40.1654	30.3547
7	3.3238	-0.504	-0.1764	3.2417	6.7298	7.4439	-0.0027	0.067	-0.0278	-0.0623	0.293	0.065	-0.0744	0.2575	-0.2903	0.0867	0.0159	0.0113	0.0224	0.046	0.1201	27.3189	42.4723	40.5386
8	12.9927	-1.4206	-0.6334	14.5378	8.2391	7.2242	-0.1678	-0.154	-0.2085	0.6865	-0.0833	-0.0671	0.0057	-0.0903	0.251	0.1113	0.029	0.025	0.1103	0.0075	0.0428	27.8025	45.6468	51.1944
9	-4.0079	-0.4798	3.7232	5.6589	9.5998	10.8558	0.1479	-0.2643	-0.3757	-0.0469	0.0355	-0.285	0.1286	-0.4581	-0.1834	0.1006	-0.0115	-0.0039	0.0939	0.0597	0.0796	27.6877	38.4855	41.7145
10	44.1811	-0.7285	-8.411	-4.6308	16.0585	1.6091	-0.8131	1.1063	-1.6883	0.5024	-0.0796	0.6418	0.2166	-0.6872	0.8927	0.1482	0.0016	-0.012	0.2304	0.0932	0.2124	15.6678	37.9056	35.9291
11	18.4289	-0.5154	0.384	5.8429	5.9497	45.2755	-0.2824	-0.1605	0.0596	-0.3608	-0.0978	0.7459	-0.5369	-1.6094	0.3802	0.083	0.0507	-0.0417	0.2151	0.0775	0.232	8.7963	45.5228	37.9836
12	-5.1676	-3.7035	6.2874	-5.3265	2.8283	13.9291	0.447	0.4654	-0.4608	0.9836	-0.5647	0.8737	0.3762	0.7421	0.1177	0.0934	0.0372	-0.0502	0.185	0.0019	0.2335	17.5223	39.6796	44.2561
13	9.0325	7.9732	10.6922	38.4138	14.8082	10.2353	0.0505	-0.0991	-0.1659	-0.2765	-0.1562	0.1902	0.1871	-0.3549	0.1057	0.0965	-0.0052	0.0531	0.1138	0.0473	0.1754	22.7529	33.2499	48.7344
14	0.9408	10.1648	0.0538	6.5198	-3.9271	6.408	-0.0225	-0.3047	-0.0725	-0.1447	0.018	0.6575	0.1105	-0.1703	0.0045	0.0931	0.0278	0.0336	0.1475	0.0442	0.1377	20.0892	42.6657	51.3521
15	4.5637	-0.7139	-6.107	0.8343	1.0922	13.6322	0.1282	0.1271	0.2664	-0.0732	0.2104	-0.0251	-0.1705	-0.027	-0.3385	0.1208	0.0187	-0.0143	0.0771	0.0392	0.1123	28.6492	45.8605	34.5381
16	26.3325	-5.5146	-8.6865	25.133	-4.414	18.7256	0.5585	0.9988	0.5187	-1.3174	0.0066	-0.3741	-0.5384	0.9963	-0.5651	0.3129	-0.0239	0.0574	0.2276	0.0686	0.1543	38.8935	50.9742	20.8536
17	45.9604	4.5155	-10.6599	-19.5942	6.7437	25.1787	1.625	-0.284	2.2931	-0.44	-0.2828	0.1009	-2.2464	-0.3739	-1.3422	0.3802	0.0469	0.1507	0.1563	0.17	0.3743	30.1506	53.9048	25.8089
18	16.7293	4.9472	-14.2208	-2.1957	-3.0906	25.0707	0.5756	-0.7755	0.7007	0.005	-0.4656	-0.0082	-1.3143	0.2867	-0.11	0.2818	0.0924	-0.0078	0.1572	0.101	0.3704	20.3429	54.9353	37.2792
19	29.3049	9.5874	11.2733	84.7759	-35.2481	52.0248	0.6038	-1.2148	1.8545	1.704	-0.4443	2.8459	-2.5709	-0.8106	-0.1595	0.2868	0.1057	0.0737	0.3225	-0.0606	0.3849	12.3664	53.4373	44.4127
20	15.0195	-14.1937	4.7118	26.3363	-27.958	37.1547	-0.1369	0.1537	0.6136	-0.1531	-0.7466	-1.3509	-0.2908	1.1921	0.8835	0.3285	0.1955	-0.0179	0.3977	0.0917	0.2826	15.889	59.5567	35.4456

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	1 - 18	1 - 18
2	X-RAY DIFFRACTION	2	A	A	19 - 20	19 - 20
3	X-RAY DIFFRACTION	3	A	A	21 - 26	21 - 26
4	X-RAY DIFFRACTION	4	A	A	27 - 29	27 - 29
5	X-RAY DIFFRACTION	5	A	A	30 - 36	30 - 36
6	X-RAY DIFFRACTION	6	A	A	37 - 42	37 - 42
7	X-RAY DIFFRACTION	7	A	A	43 - 48	43 - 48
8	X-RAY DIFFRACTION	8	A	A	49 - 53	49 - 53
9	X-RAY DIFFRACTION	9	A	A	54 - 58	54 - 58
10	X-RAY DIFFRACTION	10	A	A	59 - 62	59 - 62
11	X-RAY DIFFRACTION	11	A	A	63 - 68	63 - 68
12	X-RAY DIFFRACTION	12	A	A	69 - 72	69 - 72
13	X-RAY DIFFRACTION	13	A	A	73 - 77	73 - 77
14	X-RAY DIFFRACTION	14	A	A	78 - 83	78 - 83
15	X-RAY DIFFRACTION	15	A	A	84 - 94	84 - 94
16	X-RAY DIFFRACTION	16	A	A	95 - 99	95 - 99
17	X-RAY DIFFRACTION	17	A	A	100 - 103	100 - 103
18	X-RAY DIFFRACTION	18	A	A	104 - 109	104 - 109
19	X-RAY DIFFRACTION	19	A	A	110 - 113	110 - 113
20	X-RAY DIFFRACTION	20	A	A	114 - 117	114 - 117

Refinement

*PLUS

R_factor R_free: 0.204 / R_factor R_work: 0.161

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.017
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.56

LS refinement shell

*PLUS

R_factor R_free: 0.206 / R_factor R_work: 0.177

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