PDB-4rm1: The crystal structure of Y333Q mutant pyridoxal-dependent decarbo...

ID or keywords:

Entry

Database: PDB / ID: 4rm1

Title

The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus DSM 20745

Components

Pyridoxal-dependent decarboxylase

Keywords

LYASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / A/B/A FOLD / CYTOSOLIC

Function / homology

Function and homology information

sulfinoalanine decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Sphaerobacter thermophilus DSM 20745 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus DSM 20745
Authors: Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Oct 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rm1.cif.gz	748.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4rm1.ent.gz	636.2 KB	Display	PDB format
PDBx/mmJSON format	4rm1.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/rm/4rm1 ftp://data.pdbj.org/pub/pdb/validation_reports/rm/4rm1	HTTPS FTP

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Related structure data

Similar structure data	4rlg-1 4riz-1 4riz-2 4rlg-2 5o5c-1 4rj0-1 4rj0-2 5uzr-d 4quo-d 4qhp-d Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: MCSG-APC100677

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Pyridoxal-dependent decarboxylase

A: Pyridoxal-dependent decarboxylase

C: Pyridoxal-dependent decarboxylase

D: Pyridoxal-dependent decarboxylase

hetero molecules

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

1

B: Pyridoxal-dependent decarboxylase

A: Pyridoxal-dependent decarboxylase

hetero molecules

defined by author&software
107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Pyridoxal-dependent decarboxylase

D: Pyridoxal-dependent decarboxylase

hetero molecules

defined by author&software
106 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.548, 125.004, 132.242
Angle α, β, γ (deg.)	90.00, 99.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyridoxal-dependent decarboxylase Mass: 53080.449 Da / Num. of mol.: 4 / Mutation: Y333Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria) Gene: Sthe_2364 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D1C7D8, glutamate decarboxylase
#2: Chemical	ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₃N₂O₅P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.67 Å³/Da / Density % sol: 53.92 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2014 / Details: MIRRORS
Radiation	Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 1.99→50 Å / Num. all: 149304 / Num. obs: 151087 / % possible obs: 98.8 % / Redundancy: 2.7 % / B_iso Wilson estimate: 23.67 Å² / R_sym value: 0.085 / Net I/σ(I): 6.9
Reflection shell	Resolution: 1.99→2.02 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / R_sym value: 0.566 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→45.117 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2029	7247	4.94 %
R_work	0.1688	-	-
obs	0.1705	146599	95.48 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.99→45.117 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14501	0	70	1116	15687

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	14913
X-RAY DIFFRACTION	f_angle_d	1.226	20290
X-RAY DIFFRACTION	f_dihedral_angle_d	13.961	5455
X-RAY DIFFRACTION	f_chiral_restr	0.06	2279
X-RAY DIFFRACTION	f_plane_restr	0.006	2667

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 (%)
1.99-2.0075	0.2545	206	0.2106	3515	X-RAY DIFFRACTION	74
2.0075-2.0311	0.2622	196	0.2054	4341	X-RAY DIFFRACTION	89
2.0311-2.0559	0.2421	239	0.2017	4349	X-RAY DIFFRACTION	90
2.0559-2.0819	0.2417	231	0.1932	4397	X-RAY DIFFRACTION	92
2.0819-2.1093	0.2186	256	0.1968	4534	X-RAY DIFFRACTION	93
2.1093-2.1382	0.2519	210	0.1933	4498	X-RAY DIFFRACTION	93
2.1382-2.1687	0.2375	236	0.1915	4542	X-RAY DIFFRACTION	93
2.1687-2.2011	0.2722	227	0.1883	4530	X-RAY DIFFRACTION	93
2.2011-2.2355	0.2186	241	0.1877	4548	X-RAY DIFFRACTION	94
2.2355-2.2721	0.2264	235	0.1905	4586	X-RAY DIFFRACTION	95
2.2721-2.3113	0.244	240	0.1853	4659	X-RAY DIFFRACTION	95
2.3113-2.3533	0.2538	190	0.1842	4664	X-RAY DIFFRACTION	96
2.3533-2.3986	0.2066	242	0.1769	4740	X-RAY DIFFRACTION	97
2.3986-2.4475	0.1951	237	0.1823	4689	X-RAY DIFFRACTION	97
2.4475-2.5008	0.234	259	0.1821	4785	X-RAY DIFFRACTION	98
2.5008-2.5589	0.2326	249	0.179	4740	X-RAY DIFFRACTION	98
2.5589-2.6229	0.213	238	0.1783	4806	X-RAY DIFFRACTION	99
2.6229-2.6938	0.22	260	0.185	4789	X-RAY DIFFRACTION	99
2.6938-2.7731	0.2065	278	0.1799	4774	X-RAY DIFFRACTION	99
2.7731-2.8626	0.207	236	0.179	4802	X-RAY DIFFRACTION	99
2.8626-2.9649	0.2217	251	0.1815	4833	X-RAY DIFFRACTION	99
2.9649-3.0836	0.2029	275	0.1735	4802	X-RAY DIFFRACTION	99
3.0836-3.2239	0.2108	241	0.1738	4827	X-RAY DIFFRACTION	99
3.2239-3.3938	0.2151	265	0.1713	4811	X-RAY DIFFRACTION	99
3.3938-3.6063	0.1892	262	0.1648	4775	X-RAY DIFFRACTION	99
3.6063-3.8846	0.169	258	0.1506	4848	X-RAY DIFFRACTION	99
3.8846-4.2753	0.1702	254	0.1381	4757	X-RAY DIFFRACTION	98
4.2753-4.8933	0.1631	265	0.1362	4794	X-RAY DIFFRACTION	98
4.8933-6.1625	0.1917	217	0.1575	4833	X-RAY DIFFRACTION	98
6.1625-45.1282	0.169	253	0.1499	4784	X-RAY DIFFRACTION	96

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	3.0546	-3.45	-0.1444	5.7428	0.2942	2.3492	0.1854	0.3038	0.0558	-0.6195	-0.1535	0.021	-0.2319	-0.1897	-0.0162	0.2208	-0.0274	0.0078	0.2069	0.0233	0.1148	20.1335	-0.6155	30.0653
2	1.72	-3.2621	0.2644	8.0149	-1.1734	0.1916	0.0312	0.0637	0.1824	-0.275	-0.0789	-0.4591	-0.0094	0.1779	0.1247	0.1592	-0.0349	0.063	0.2648	0.0278	0.2045	37.7804	-5.0904	37.4663
3	0.3154	-0.4302	0.1648	0.7334	-0.3175	0.8633	-0.0108	0.0052	-0.1284	-0.0493	0.0379	0.0838	0.0544	-0.0588	-0.0373	0.0882	-0.0237	-0.0045	0.1236	-0.0015	0.1547	20.37	-21.6892	50.2641
4	4.2286	-3.4472	-0.3966	5.127	0.8122	1.9156	-0.0251	-0.2255	-0.1241	0.2849	0.0471	-0.053	-0.021	-0.0164	-0.031	0.1544	-0.0318	-0.0421	0.139	0.0191	0.0986	26.1633	-19.9859	74.282
5	1.0344	-0.0623	-0.0374	2.0049	0.6447	1.7478	-0.0439	-0.1714	-0.1057	0.2726	0.0417	-0.1516	0.1619	0.1648	0.0156	0.1193	0.0079	-0.0166	0.1412	0.0402	0.1636	32.066	-32.782	69.4212
6	3.9198	-0.9489	-2.1745	2.326	-1.5227	4.0573	-0.0429	0.0059	-0.1331	-0.0558	0.003	0.0391	0.1904	-0.0325	0.0421	0.0718	-0.0579	-0.0393	0.1262	-0.0203	0.1313	25.0775	-30.956	55.5417
7	0.5668	0.2218	0.9305	1.4197	-0.011	1.6723	-0.0404	-0.0872	0.0574	0.1094	0.0152	0.4082	-0.0396	-0.4899	0.0372	0.0824	-0.0138	0.0242	0.213	0.0172	0.2136	11.3061	-18.8548	55.9192
8	6.512	-0.6822	1.6512	1.3572	-0.639	1.532	0.0713	0.2825	-0.4984	-0.1801	-0.0755	-0.2726	0.289	0.2423	-0.1555	0.1912	0.0278	0.0741	0.1746	0.0164	0.2709	41.5727	-36.7157	47.0503
9	4.77	0.1103	1.0093	1.3504	-0.3502	1.7092	-0.0017	0.075	-0.0212	-0.0975	-0.0948	-0.4047	-0.0314	0.4242	0.149	0.1402	0.0033	0.0428	0.1997	0.0417	0.32	53.3424	-26.5022	49.9386
10	4.8241	-1.0568	-0.6859	3.3904	0.6137	3.7307	0.3107	0.4947	-0.8318	-0.722	-0.3184	0.0923	0.5668	0.2303	0.0096	0.3111	-0.0314	0.0121	0.2033	-0.0298	0.2172	26.9837	-23.1662	29.2267
11	2.0234	-2.5231	-0.5275	6.9205	1.8902	0.5828	0.0612	0.2053	-0.362	-0.3326	-0.1796	0.685	0.1074	-0.1425	0.1218	0.1653	-0.0416	-0.0408	0.2217	-0.0069	0.1999	9.505	-15.4756	39.0115
12	0.0521	-0.2557	-0.4265	0.7004	0.2525	1.6812	0.0058	-0.0025	0.0907	-0.0093	0.0324	-0.1878	-0.0258	0.081	-0.0396	0.0643	-0.0221	0.0085	0.1339	0.0016	0.1606	31.2227	-4.2475	54.1032
13	8.2935	-7.6448	3.3024	7.4897	-3.139	4.4902	-0.3568	-0.6104	-0.1094	0.6224	0.5174	0.122	-0.2487	-0.0367	-0.1876	0.1732	-0.0841	0.0308	0.1944	-0.0203	0.169	21.0931	-5.8153	76.4121
14	1.73	-1.2287	0.3922	2.8514	-1.106	1.4489	-0.0837	-0.2778	0.069	0.385	0.09	0.1843	-0.0987	-0.1268	-0.0038	0.1245	-0.0171	0.0386	0.1816	-0.0124	0.1431	13.333	2.3761	72.6088
15	3.3217	-0.7909	3.3077	2.8853	-0.9389	9.7931	-0.1121	0.0209	0.1831	0.073	-0.058	0.1015	-0.4379	-0.0451	0.1977	0.0299	-0.021	0.0336	0.0759	-0.0086	0.1592	19.7158	10.8068	62.3961
16	0.0051	-0.0537	-0.166	1.266	-0.1295	1.1062	-0.0105	-0.0276	0.048	0.061	-0.0163	-0.245	0.0068	0.1904	0.0244	0.0758	-0.0132	0.0001	0.1564	-0	0.1643	30.5736	-2.9426	58.4087
17	5.5165	-0.0849	-1.7461	1.0357	0.2487	1.1594	0.0752	-0.0238	0.2705	-0.023	0.0005	0.2721	-0.08	-0.1948	-0.085	0.1157	0.0164	-0.0261	0.1958	0.0323	0.1395	1.697	5.2436	50.2271
18	4.0935	0.3522	-2.617	2.188	-0.3231	3.7222	0.1277	0.1162	0.099	-0.1221	0.0115	0.4118	-0.0382	-0.4637	-0.1252	0.0914	-0.0124	-0.0262	0.1648	0.0011	0.2217	-3.1354	2.2354	47.9116
19	1.0226	0.8443	-0.5112	3.3112	-1.4443	0.9111	0.0095	-0.0846	-0.2474	0.0775	-0.174	-0.4751	0.0927	0.1537	0.1817	0.2431	0.0314	-0.0489	0.2272	0.0145	0.2147	24.204	35.1968	18.9605
20	0.6875	0.0001	0.208	1.9772	-0.5791	1.4446	0.0368	0.0198	0.0592	-0.1418	0.0303	0.2779	-0.0116	-0.1095	-0.0866	0.2421	0.0279	-0.0151	0.1406	-0.006	0.164	-0.2045	50.7813	7.5869
21	1.0412	0.3012	0.2686	1.6128	-0.0839	1.1711	0.0182	0.2507	0.0939	-0.5739	0.0302	0.2133	-0.0377	-0.0553	-0.0107	0.4418	0.0339	-0.0437	0.2249	0.024	0.2069	3.0822	60.0208	-10.858
22	1.4761	0.276	0.8723	2.579	-0.5191	1.2233	0.0225	-0.1428	0.1632	0.0287	0.0115	0.3039	-0.0897	-0.1171	-0.0588	0.2778	0.0455	0.0069	0.1483	-0.019	0.1375	1.5543	56.2005	7.7367
23	2.5137	0.0805	-2.2901	1.1406	-0.7542	4.5522	0.1427	0.0757	0.1294	-0.1532	-0.1529	-0.328	-0.1254	0.3602	-0.0097	0.2583	0.0104	0.0127	0.2026	0.0266	0.2249	28.6472	59.5379	-1.5226
24	5.1956	3.9011	-2.308	5.2208	-2.843	4.6455	0.3643	-0.6165	-0.2061	0.94	-0.4744	-0.5684	-0.524	0.5495	0.1016	0.4079	-0.0111	-0.1138	0.3017	-0.0009	0.236	24.385	50.1369	27.268
25	1.4324	2.9288	-0.4549	8.5384	-0.3134	0.8427	0.2208	-0.2462	0.3242	0.9966	-0.1142	0.526	-0.3168	0.0329	-0.0915	0.4323	0.0201	0.0246	0.2567	-0.0261	0.1828	4.8199	45.1933	29.4845
26	2.2101	0.6606	1.4523	1.6056	0.3862	1.5333	-0.0516	0.1811	-0.0599	-0.2493	0.0208	-0.0862	0.0642	0.1299	0.0211	0.2595	0.0297	0.0245	0.1406	0.0066	0.1118	12.7902	33.8962	3.8695
27	4.1152	4.4343	-2.9626	7.3921	-7.2288	9.3445	-0.1546	0.506	0.225	-0.8042	0.6767	0.7917	0.1099	-0.675	-0.4056	0.4731	0.0651	-0.1254	0.2161	-0.0449	0.3364	-9.0872	35.3367	-6.9314
28	1.3667	0.4794	0.2781	2.6001	-0.3186	2.431	-0.0235	0.1477	-0.0717	-0.3881	0.0922	0.5337	0.2281	-0.2409	-0.0811	0.2906	-0.0237	-0.0788	0.1724	-0.004	0.2457	-8.1732	23.9559	2.2592
29	1.529	0.3276	1.6149	3.9276	-0.219	2.5804	-0.116	0.3305	-0.0277	-0.6301	0.0286	-0.3746	-0.0216	0.3417	0.1253	0.3135	0.0357	0.0346	0.2066	-0.0012	0.17	9.6198	32.8271	0.6997
30	5.1641	0.842	-1.8382	1.7787	-0.507	2.1106	-0.0665	-0.0503	-0.1765	0.1864	0.0699	0.3434	-0.03	-0.3463	0.0134	0.2903	0.0285	-0.0145	0.1948	0.03	0.1449	-7.3767	23.5954	25.2511
31	6.1455	0.2446	0.874	2.4024	0.1709	2.2822	-0.0823	-0.589	-0.112	0.4304	0.0375	0.3602	-0.2213	-0.4035	0.0472	0.3431	0.0507	0.045	0.1936	0.0378	0.2102	-9.4129	27.158	30.504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid -1 through 37 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 38 through 82 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 83 through 162 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 163 through 202 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 203 through 282 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 283 through 323 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 324 through 363 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 364 through 403 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 404 through 476 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid -1 through 38 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 39 through 96 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 97 through 167 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 168 through 191 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 192 through 254 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 255 through 289 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 290 through 355 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 356 through 435 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 436 through 477 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid -1 through 96 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 97 through 191 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 192 through 264 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 265 through 354 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 355 through 477 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 5 through 38 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 39 through 96 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 97 through 167 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 168 through 191 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 192 through 289 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 290 through 355 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 356 through 433 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 434 through 476 )

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