PDB-1ppy: Native precursor of pyruvoyl dependent Aspartate decarboxylase

ID or keywords:

Entry

Database: PDB / ID: 1ppy

Title

Native precursor of pyruvoyl dependent Aspartate decarboxylase

Components

Aspartate 1-decarboxylase precursor

Keywords

LYASE / decarboxylase / pantothenate pathway / intramolecular protein 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 17, 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	Aug 16, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1ppy.cif.gz	112.5 KB	Display	PDBx/mmCIF format
PDB format	pdb1ppy.ent.gz	88.6 KB	Display	PDB format
PDBx/mmJSON format	1ppy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1ppy_validation.pdf.gz	453.4 KB	Display	wwPDB validaton report
Full document	1ppy_full_validation.pdf.gz	455.3 KB	Display
Data in XML	1ppy_validation.xml.gz	14.5 KB	Display
Data in CIF	1ppy_validation.cif.gz	20.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pp/1ppy ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1ppy	HTTPS FTP

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Related structure data

Related structure data	1pqeC 1pqfC 1pqhC 1pt0C 1pt1C 1pyqC 1pyuC 1aw8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1pqf-1 1aw8-1 4aon-1 6oz8-1 1pt1-1 6mkb-2 6p02-2 1pyq-1 4aok-1 1pt0-1 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 precursor

B: Aspartate 1-decarboxylase precursor

hetero molecules

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

1

A: Aspartate 1-decarboxylase precursor

B: Aspartate 1-decarboxylase precursor

hetero molecules

A: Aspartate 1-decarboxylase precursor

B: Aspartate 1-decarboxylase precursor

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.983, 70.983, 216.386
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 operation: X,X-Y,1/6-Z.

#1: Protein	Aspartate 1-decarboxylase precursor / Aspartate alpha-decarboxylase precursor Mass: 13866.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAND OR B0131 OR C0160 OR Z0142 OR ECS0135 OR SF0128 / Plasmid: pBluescript KS / Production host: Escherichia coli (E. coli) / Strain (production host): SJ16 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 270 / 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: 3.1 Å³/Da / Density % sol: 59.7 %

Crystal grow

Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: NH42SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal grow

*PLUS

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

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID
1	5-9 mg/ml	protein	1	drop
2	1.6 M	ammonium sulfate	1	reservoir

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5482 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 6, 1999
Radiation	Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5482 Å / Relative weight: 1
Reflection	Resolution: 1.95→62.02 Å / Num. obs: 20348 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 17.9 % / B_iso Wilson estimate: 24.8 Å² / R_sym value: 0.058 / Net I/σ(I): 24.5
Reflection shell	Resolution: 1.95→2.01 Å / Mean I/σ(I) obs: 3.1 / R_sym value: 0.29 / % possible all: 89.3
Reflection	PLUS Lowest resolution: 62 Å / Num. obs: 24605 / R_merge(I) obs*: 0.059
Reflection shell	PLUS % possible obs: 89.3 % / R_merge(I) obs: 0.29 / Mean I/σ(I) obs*: 3.2

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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: 1.95→62.02 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.943 / SU B: 2.451 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19522	1183	5.1 %	RANDOM
R_work	0.15762	-	-	-
all	0.15941	24605	-	-
obs	0.15941	20348	95.51 %	-

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: 14.99 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9 Å²	0.45 Å²	0 Å²
2-	-	0.9 Å²	0 Å²
3-	-	-	-1.35 Å²

Refine analyze

Luzzati coordinate error free: 0.12 Å

Refinement step

Cycle: LAST / Resolution: 1.95→62.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1755	0	5	270	2030

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	1817
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	1651
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.931	2458
X-RAY DIFFRACTION	r_angle_other_deg	0.817	3	3810
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.474	5	231
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	278
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2060
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	380
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	323
X-RAY DIFFRACTION	r_nbd_other	0.253	0.2	2026
X-RAY DIFFRACTION	r_nbtor_other	0.114	0.2	1125
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.2	189
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.221	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.343	0.2	89
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.298	0.2	50
X-RAY DIFFRACTION	r_mcbond_it	0.652	1.5	1155
X-RAY DIFFRACTION	r_mcangle_it	1.085	2	1838
X-RAY DIFFRACTION	r_scbond_it	1.822	3	662
X-RAY DIFFRACTION	r_scangle_it	2.897	4.5	620

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.238	76
R_work	0.194	1462

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	5.3021	2.5572	4.1268	3.969	4.6283	7.2817	-0.1957	-0.2212	0.3517	-0.1745	0.0283	0.1349	-0.3223	0.0846	0.1674	0.0654	-0.0175	-0.0181	0.0682	0.0328	0.0861	53.9577	45.2888	26.4322
2	11.9116	-6.5232	-0.0422	12.6439	-2.3636	23.2658	0.1199	-1.0604	-0.3751	1.378	-0.1007	-0.6382	1.0953	1.8584	-0.0193	0.3689	-0.0003	-0.1408	0.4316	0.0052	0.2629	64.7555	38.0072	40.0966
3	5.7295	-0.8339	-0.5909	19.3858	5.2552	-7.4007	0.0809	-0.0261	0.2991	0.6011	-0.067	-0.5774	0.5434	0.1631	-0.0138	0.1227	0.0201	-0.0545	0.1769	0.0008	0.0758	56.4985	43.4898	38.1878
4	8.3097	1.9132	9.2866	4.8618	-0.2392	9.8464	0.0441	-0.3523	0.1387	0.095	-0.1212	0.3381	-0.0759	-0.2529	0.0772	0.0982	-0.0055	-0.0015	0.1341	-0.0321	0.0982	49.8913	44.7009	37.0897
5	1.2951	0.5277	0.8844	4.2878	2.4213	2.0435	-0.1165	-0.1042	0.0518	0.0183	0.1276	-0.096	0.0018	0.2408	-0.011	0.0681	-0.0144	-0.0507	0.1364	-0.009	0.0933	58.2802	42.8599	32.4337
6	31.8552	-40.1723	-4.858	55.4765	-1.1487	10.3442	-0.2544	0.3849	0.2285	0.3278	0.3858	-1.6509	0.3441	0.9453	-0.1314	0.0616	-0.09	-0.0533	0.2655	-0.0462	0.2229	63.8422	44.4439	37.1163
7	-23.0121	-40.2582	39.1804	70.1145	-62.2734	59.4149	0.3226	0.3648	-0.8147	1.1061	-0.4858	-0.3599	1.3601	1.6781	0.1632	0.3834	-0.0121	-0.0653	0.4753	-0.1889	0.5527	71.3112	40.2224	34.2318
8	2.7027	2.9854	3.6554	3.0088	3.6434	4.8699	-0.1571	-0.1354	0.2822	-0.162	-0.1273	0.2301	-0.3352	-0.1757	0.2844	0.1314	-0.0081	-0.0261	0.1274	0.0146	0.1086	51.0658	47.489	26.8801
9	1.4678	-0.4593	0.6377	4.9655	-0.633	1.721	-0.0097	0.1122	0.242	-0.3386	-0.064	-0.1643	-0.1765	0.2015	0.0737	0.0846	-0.0383	0.0027	0.1301	0.0311	0.1141	55.8738	39.396	5.505
10	21.8957	12.993	-7.2879	18.4125	-6.1956	55.3038	1.3746	-2.5592	1.6125	2.5826	-0.5024	-0.1644	-2.9172	0.9683	-0.8722	0.4804	-0.0139	0.0056	0.4459	-0.1547	0.5169	57.3709	56.2744	17.0527
11	11.485	-0.0994	8.1329	26.0283	-3.4383	14.3919	0.3087	-0.113	0.6666	-0.0643	0.1056	0.0507	-0.5594	-0.3115	-0.4144	0.2224	-0.0487	0.029	0.0452	0.076	0.2004	51.4354	52.8482	8.5171
12	0.1345	1.1949	-4.4196	6.7228	6.2314	7.4237	0.0457	0.6166	0.4759	-0.0114	-0.174	0.2027	-0.42	-0.1409	0.1283	0.1831	-0.0141	-0.0741	0.1149	0.0951	0.1736	47.5603	49.4279	4.1371
13	3.7625	-0.1101	-0.4699	2.0398	-0.7107	3.7844	-0.0404	0.0936	0.5629	-0.1413	-0.0333	-0.2606	-0.4823	0.1953	0.0737	0.1751	-0.0673	-0.0482	0.0804	0.0324	0.1919	55.3817	48.4697	10.0534
14	25.3608	-6.5331	-3.4069	25.9112	-13.1538	62.4897	-0.0253	-1.343	-0.3505	1.6394	0.2448	0.2685	-1.4014	1.5053	-0.2195	0.2949	-0.1442	0.009	0.2127	0.0612	0.3835	57.5809	54.4379	11.6289
15	25.9422	20.7855	3.289	15.7302	-6.4153	78.033	-0.4315	-0.9139	2.5836	1.3591	0.1048	-0.0395	-0.0661	-1.316	0.3267	0.4887	-0.0781	-0.0837	0.4088	0.0041	0.4678	64.2961	52.8301	17.3697
16	3.2061	2.2858	0.0794	7.2614	-0.3706	2.3669	-0.0907	0.3423	0.3301	-0.6843	0.0743	0.039	-0.2576	0.2121	0.0164	0.1396	-0.0093	0.0069	0.1472	0.0407	0.1267	54.1637	40.6055	2.7479

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 - 19	1 - 19
2	X-RAY DIFFRACTION	2	A	A	20 - 26	20 - 26
3	X-RAY DIFFRACTION	3	A	A	27 - 29	27 - 29
4	X-RAY DIFFRACTION	4	A	A	30 - 36	30 - 36
5	X-RAY DIFFRACTION	5	A	A	37 - 68	37 - 68
6	X-RAY DIFFRACTION	6	A	A	69 - 72	69 - 72
7	X-RAY DIFFRACTION	7	A	A	73 - 77	73 - 77
8	X-RAY DIFFRACTION	8	A	A	78 - 118	78 - 118
9	X-RAY DIFFRACTION	9	B	B	1 - 16	1 - 16
10	X-RAY DIFFRACTION	10	B	B	17 - 26	17 - 26
11	X-RAY DIFFRACTION	11	B	B	27 - 29	27 - 29
12	X-RAY DIFFRACTION	12	B	B	30 - 36	30 - 36
13	X-RAY DIFFRACTION	13	B	B	37 - 68	37 - 68
14	X-RAY DIFFRACTION	14	B	B	69 - 72	69 - 72
15	X-RAY DIFFRACTION	15	B	B	73 - 79	73 - 79
16	X-RAY DIFFRACTION	16	B	B	80 - 115	80 - 115

Refinement

*PLUS

Num. reflection obs: 22229 / R_factor R_free: 0.202 / R_factor R_work: 0.159

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.014
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.6

LS refinement shell

*PLUS

R_factor R_free: 0.23 / R_factor R_work: 0.196

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