PDB-1pyq: Unprocessed Aspartate Decarboxylase Mutant, with Alanine inserted...

ID or keywords:

Entry

Database: PDB / ID: 1pyq

Title

Unprocessed Aspartate Decarboxylase Mutant, with Alanine inserted at position 24

Components

Aspartate 1-decarboxylase

Keywords

LYASE / Autoprocessing / 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 /

SYNCHROTRON /

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	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_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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1pyq.cif.gz	110.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1pyq.ent.gz	87.1 KB	Display	PDB format
PDBx/mmJSON format	1pyq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	1pyq_validation.pdf.gz	447.5 KB	Display	wwPDB validaton report
Full document	1pyq_full_validation.pdf.gz	447.8 KB	Display
Data in XML	1pyq_validation.xml.gz	12.9 KB	Display
Data in CIF	1pyq_validation.cif.gz	18 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/py/1pyq ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyq	HTTPS FTP

-
Related structure data

Related structure data	1ppyC 1pqeC 1pqfC 1pqhC 1pt0C 1pt1C 1pyuC 1aw8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4azd-1 1aw8-1 1pt0-1 1pt1-1 6p02-2 4aon-1 2c45-2 1ppy-1 6oz8-1 2eeo-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
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

B: Aspartate 1-decarboxylase

hetero molecules

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

1

A: Aspartate 1-decarboxylase

B: Aspartate 1-decarboxylase

hetero molecules

A: Aspartate 1-decarboxylase

B: Aspartate 1-decarboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.911, 70.911, 218.665
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	Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase Mass: 15850.979 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: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal

Density Matthews: 2.5 Å³/Da / Density % sol: 50.8 %

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 ℃ / 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

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2002 / Details: vertical focusing mirror
Radiation	Monochromator: Si 111, bent, triangular, liquid gallium cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 1.9→25 Å / Num. all: 26521 / Num. obs: 25960 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.32 % / B_iso Wilson estimate: 33.3 Å² / R_sym value: 0.051 / Net I/σ(I): 45.78
Reflection shell	Resolution: 1.9→1.949 Å / Mean I/σ(I) obs: 9.65 / Num. unique all: 1815 / R_sym value: 0.298 / % possible all: 100
Reflection	PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Num. obs: 26749 / % possible obs: 99.4 % / Redundancy: 29.3 % / R_merge(I) obs*: 0.051
Reflection shell	PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.94 Å / % possible obs: 100 % / R_merge(I) obs: 0.298 / Mean I/σ(I) obs*: 9.6

-
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→25 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.96 / SU B: 2.126 / SU ML: 0.063 / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.109 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17891	1337	5 %	RANDOM
R_work	0.16633	-	-	-
obs	0.16697	25184	99.5 %	-
all	-	26521	-	-

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: 13.809 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0.11 Å²	0 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	-0.34 Å²

Refine analyze

Luzzati coordinate error obs: 0.207 Å

Refinement step

Cycle: LAST / Resolution: 1.9→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1771	0	20	172	1963

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	1839
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	1646
X-RAY DIFFRACTION	r_angle_refined_deg	1.531	1.927	2493
X-RAY DIFFRACTION	r_angle_other_deg	0.825	3	3801
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.946	5	234
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	282
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2090
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	380
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	333
X-RAY DIFFRACTION	r_nbd_other	0.253	0.2	1924
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	1130
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.222	0.2	110
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.217	0.2	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.337	0.2	71
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.207	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	0.733	1.5	1168
X-RAY DIFFRACTION	r_mcangle_it	1.292	2	1858
X-RAY DIFFRACTION	r_scbond_it	2.207	3	671
X-RAY DIFFRACTION	r_scangle_it	3.584	4.5	635

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection
R_free	0.256	94
R_work	0.196	1815
obs	-	1815

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	33.7383	10.5494	24.2801	86.4625	5.5203	9.9044	0.7809	-1.2911	-1.0426	1.3144	-0.2478	4.1107	0.6966	-1.7311	-0.5331	0.1605	-0.1217	0.0164	0.3913	0.0243	0.3675	40.2198	29.323	10.8233
2	5.1691	3.7089	5.7289	2.6153	5.3938	8.9154	-0.1175	0.0172	0.2726	-0.1174	0.0261	0.0444	-0.2791	0.2494	0.0914	0.1058	-0.0285	-0.0255	0.0497	0.0095	0.0763	55.0084	45.6843	27.6921
3	147.2653	9.2413	48.2376	10.4694	5.1393	30.0556	1.5496	-3.8037	-4.3435	1.9774	0.3353	-0.4661	1.2108	0.7206	-1.8848	0.5609	0.0905	-0.1307	0.4565	0.0321	0.4631	68.7691	36.7923	38.4614
4	17.2562	-2.4814	0.5862	3.6159	7.7605	-9.47	0.0757	-0.1449	-0.131	-0.0199	0.0197	-0.3856	0.0507	-0.1122	-0.0954	0.1251	-0.0274	-0.0233	0.1071	-0.0058	0.0726	58.2841	41.8754	36.7905
5	10.3437	0.9335	8.932	1.45	3.147	13.3775	0.2453	-0.3344	-0.0311	0.3412	-0.1307	0.4112	0.003	-0.3214	-0.1146	0.1303	-0.0549	0.0081	0.1046	-0.0339	0.0582	50.2774	44.5924	38.4136
6	1.9564	1.2654	1.2951	4.3423	1.5231	1.3715	-0.0852	-0.0248	-0.0458	-0.0145	0.0262	-0.1272	0.0477	0.1319	0.059	0.0895	-0.0201	-0.0451	0.0865	0.0078	0.0647	58.1027	42.6907	32.1013
7	8.9251	-3.227	2.1181	9.8936	2.9373	0.5379	-0.0768	-0.1215	-0.1215	0.0837	0.0684	-0.4547	0.0215	0.391	0.0084	0.1021	-0.0245	-0.0196	0.1091	-0.0287	0.0771	61.471	45.2536	38.4423
8	18.3527	-4.9917	4.3361	-10.4023	15.6037	-7.4928	-0.514	-0.2233	-1.3275	0.4422	0.4367	0.0184	0.5185	0.9825	0.0773	0.2388	0.023	-0.0334	0.2346	-0.0539	0.3026	68.81	39.5467	34.3134
9	1.9031	2.2271	2.7106	2.3107	2.7572	4.3204	-0.0848	-0.1088	0.223	-0.0614	-0.1502	0.1779	-0.2316	-0.2476	0.2349	0.1247	-0.0178	-0.0359	0.0899	0.0029	0.0842	51.6667	46.7527	27.1138
10	4.0224	2.6646	-0.055	9.9551	-1.609	3.2559	-0.1191	0.1966	0.448	-0.496	-0.0227	-0.2102	-0.306	0.1856	0.1418	0.0524	-0.0145	0.0021	0.1297	0.0441	0.0746	55.9074	41.7256	6.0988
11	14.3476	-2.7043	10.2651	14.4786	2.1386	30.9566	-0.1606	-0.7288	2.0506	0.5508	-0.5257	-0.447	-1.6943	-2.1297	0.6863	0.4393	-0.0071	0.0156	0.4143	0.0282	0.4528	53.9432	56.9736	18.7368
12	5.644	8.2087	19.8103	-4.0254	-6.4732	23.3452	0.003	-0.1526	-0.0512	-0.0869	0.2863	0.1589	-0.4397	-0.0377	-0.2893	0.1998	0.0032	0.0466	0.0752	0.0677	0.2463	53.2487	51.7845	11.0992
13	3.7647	0.1399	0.9085	13.7669	6.8216	7.3764	-0.2073	0.4641	0.7396	0.0248	0.0107	0.6405	-0.433	-0.3503	0.1966	0.2	0.0272	-0.0496	0.1144	0.1398	0.2062	47.5891	50.6935	4.7329
14	5.3779	1.4358	-0.9849	2.4797	-0.5466	4.0242	0.0152	0.0452	0.5697	-0.119	0.0945	-0.1124	-0.4336	0.0493	-0.1097	0.1692	-0.0238	-0.0132	0.0525	0.0371	0.1142	55.367	47.8598	10.186
15	15.8275	19.5205	17.4392	6.0463	3.0306	26.3816	-0.399	0.6506	0.8022	0.1238	0.4919	0.4038	-0.8576	0.8327	-0.0929	0.2853	-0.0197	0.0378	0.1308	0.1111	0.2878	56.5277	55.1983	9.7364
16	-40.5554	11.5666	27.4026	14.2998	-9.7899	8.1465	-0.1541	-1.3801	0.3078	1.1875	0.6868	-1.7964	-1.1847	0.533	-0.5327	0.6371	-0.0621	-0.0298	0.577	0.0341	0.5612	63.5414	53.0555	18.1848
17	3.6683	2.7291	-0.0488	7.1174	0.2356	2.2051	-0.1152	0.5087	0.3212	-0.6585	0.1484	0.0485	-0.3374	0.0887	-0.0332	0.1299	0.0003	0.0044	0.1701	0.0637	0.087	54.1103	40.7497	2.878

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 - 1	14 - 18
2	X-RAY DIFFRACTION	2	A	A	2 - 19	19 - 36
3	X-RAY DIFFRACTION	3	A	A	20 - 26	37 - 43
4	X-RAY DIFFRACTION	4	A	A	27 - 29	44 - 46
5	X-RAY DIFFRACTION	5	A	A	30 - 36	47 - 53
6	X-RAY DIFFRACTION	6	A	A	37 - 68	54 - 85
7	X-RAY DIFFRACTION	7	A	A	69 - 72	86 - 89
8	X-RAY DIFFRACTION	8	A	A	73 - 77	90 - 94
9	X-RAY DIFFRACTION	9	A	A	78 - 116	95 - 133
10	X-RAY DIFFRACTION	10	B	B	1 - 19	18 - 36
11	X-RAY DIFFRACTION	11	B	B	20 - 26	37 - 43
12	X-RAY DIFFRACTION	12	B	B	27 - 29	44 - 46
13	X-RAY DIFFRACTION	13	B	B	30 - 36	47 - 53
14	X-RAY DIFFRACTION	14	B	B	37 - 68	54 - 85
15	X-RAY DIFFRACTION	15	B	B	69 - 72	86 - 89
16	X-RAY DIFFRACTION	16	B	B	73 - 79	90 - 96
17	X-RAY DIFFRACTION	17	B	B	80 - 116	97 - 133

Refinement

*PLUS

R_factor R_free: 0.183 / 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

-
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