PDB-4iws: Putative Aromatic Acid Decarboxylase

ID or keywords:

Entry

Database: PDB / ID: 4iws

Title

Putative Aromatic Acid Decarboxylase

Components

PA0254

Keywords

LYASE / UbiD like split beta-barrel domain / 3-polyprenyl-4-hydroxybenzoate decarboxylase hudA

Function / homology

Function and homology information

pyrrole-2-carboxylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / : /

metal ion binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Jacewicz, A. / Izumi, A. / Brunner, K. / Schneider, G.

Citation

Journal: Plos One / Year: 2013
Title: Structural Insights into the UbiD Protein Family from the Crystal Structure of PA0254 from Pseudomonas aeruginosa.
Authors: Jacewicz, A. / Izumi, A. / Brunner, K. / Schnell, R. / Schneider, G.

History

Deposition	Jan 24, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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

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Download

PDBx/mmCIF format	4iws.cif.gz	746.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4iws.ent.gz	618.5 KB	Display	PDB format
PDBx/mmJSON format	4iws.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/iw/4iws ftp://data.pdbj.org/pub/pdb/validation_reports/iw/4iws	HTTPS FTP

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Related structure data

Related structure data	4ip2SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6evb-1 6ev6-1 6r30-1 7abn-2 7abo-1 6r3l-1 6eve-3 6e5y-1 6r3n-1 6r3f-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA0254

B: PA0254

C: PA0254

D: PA0254

hetero molecules

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

1

A: PA0254

B: PA0254

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

2

C: PA0254

D: PA0254

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.297, 55.818, 198.422
Angle α, β, γ (deg.)	90.00, 90.87, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PA0254 Mass: 57123.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0254 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9I6N5, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.53 Å³/Da / Density % sol: 51.33 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1 M (NH4)2SO4, 0.1 M Bis-Tris, 1% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2011
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.3→49.6 Å / Num. all: 102239 / Num. obs: 101115 / % possible obs: 98.9 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 4.1 / Redundancy: 3.1 % / B_iso Wilson estimate: 25.3 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.059 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 3 % / R_merge(I) obs: 0.244 / Mean I/σ(I) obs: 4.1 / R_sym value: 0.244 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
DNA		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4IP2

4ip2

Resolution: 2.3→49.212 Å / Isotropic thermal model: Anisotropic / σ(F): 4.1 / σ(I): 4.1 / Phase error: 26.99 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2191	5145	5.09 %	RANDOM
R_work	0.1643	-	-	-
obs	0.1668	101106	98.66 %	-
all	-	102479	-	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 14.346 Å² / k_sol: 0.346 e/Å³

Displacement parameters

B_iso mean: 26.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.3838 Å²	-0 Å²	2.2037 Å²
2-	-	-3.9518 Å²	-0 Å²
3-	-	-	4.3356 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→49.212 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15317	0	5	247	15569

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15745
X-RAY DIFFRACTION	f_angle_d	1.1	21498
X-RAY DIFFRACTION	f_dihedral_angle_d	14.049	5700
X-RAY DIFFRACTION	f_chiral_restr	0.073	2330
X-RAY DIFFRACTION	f_plane_restr	0.006	2858

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 (%)
2.3-2.3398	0.2849	263	0.2018	4784	X-RAY DIFFRACTION	94
2.3398-2.3824	0.2864	259	0.1991	4755	X-RAY DIFFRACTION	94
2.3824-2.4282	0.3093	260	0.1996	4894	X-RAY DIFFRACTION	95
2.4282-2.4777	0.2721	237	0.1987	4731	X-RAY DIFFRACTION	95
2.4777-2.5316	0.2691	295	0.1942	4818	X-RAY DIFFRACTION	94
2.5316-2.5905	0.2882	240	0.1928	4771	X-RAY DIFFRACTION	95
2.5905-2.6553	0.2538	264	0.1851	4826	X-RAY DIFFRACTION	94
2.6553-2.727	0.2412	231	0.1858	4755	X-RAY DIFFRACTION	95
2.727-2.8073	0.2261	266	0.1831	4857	X-RAY DIFFRACTION	94
2.8073-2.8979	0.256	226	0.1796	4814	X-RAY DIFFRACTION	95
2.8979-3.0014	0.2261	233	0.1803	4804	X-RAY DIFFRACTION	95
3.0014-3.1216	0.2375	264	0.1778	4825	X-RAY DIFFRACTION	94
3.1216-3.2636	0.2262	223	0.1722	4810	X-RAY DIFFRACTION	94
3.2636-3.4356	0.225	269	0.1608	4739	X-RAY DIFFRACTION	93
3.4356-3.6507	0.2019	263	0.1555	4805	X-RAY DIFFRACTION	93
3.6507-3.9324	0.1825	246	0.142	4813	X-RAY DIFFRACTION	93
3.9324-4.3278	0.1957	247	0.1364	4803	X-RAY DIFFRACTION	93
4.3278-4.9532	0.1591	250	0.1306	4766	X-RAY DIFFRACTION	92
4.9532-6.2374	0.1991	253	0.1542	4817	X-RAY DIFFRACTION	92
6.2374-42.6627	0.1813	249	0.1447	4850	X-RAY DIFFRACTION	91

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	0.7554	0.0171	0.0736	0.6797	0.2449	0.7009	0.0201	-0.0123	-0.0875	0.0206	-0.0268	0.1153	-0.0567	-0.0382	-0.0099	0.0741	0.0204	0.0371	0.0458	0.0169	0.1085	6.3099	-6.7075	75.2494
2	0.3717	-0.1042	-0.0616	0.2676	0.2052	0.3948	0.0264	-0.0814	0.1089	0.0838	-0.0004	0.016	-0.0853	0.0388	-0.0249	0.1668	-0.0137	0.0364	0.0788	0.0042	0.091	17.0758	2.9545	82.7003
3	0.541	-0.1542	0.1886	0.5964	-0.3524	0.4832	0.0131	0.0078	0.1039	-0.1059	-0.0585	-0.175	-0.1223	0.1162	0.0218	0.1985	-0.0187	0.053	0.0923	-0.0148	0.1221	22.9894	9.7521	85.5698
4	0.1451	-0.0504	-0.2357	0.0947	0.1978	0.5548	0.0482	-0.0503	0.0649	0.027	0.0206	-0.0131	-0.0793	0.0949	-0.0476	0.0934	0.0174	0.0216	0.0551	0.0028	0.0859	27.2654	-0.7171	71.6296
5	0.2685	0.0962	0.1033	0.2728	0.1394	0.536	-0.0029	-0.0264	0.0893	0.0239	-0.0552	0.0075	-0.0146	0.0639	0.0108	0.0541	0.0048	0.0218	0.0187	-0.0162	0.0718	30.0646	-4.1559	51.5277
6	0.6629	0.061	0.0439	0.3818	0.1328	0.4392	0.0208	-0.027	-0.04	-0.0217	0.0016	-0.0542	0.1009	-0.0554	-0.0081	0.1036	0.0026	0.0112	0.044	0.0091	0.0527	12.0182	-23.6626	31.3814
7	0.8099	0.3447	-0.0897	0.5579	0.1492	0.2716	0.0725	0.0189	-0.2787	0.1323	-0.0234	-0.2641	0.0409	0.1396	-0.0463	0.1563	0.021	-0.0078	0.1255	0.0028	0.168	25.0314	-31.5246	24.7994
8	0.229	0.0666	0.2566	0.1035	-0.0047	0.3568	0.028	0.043	-0.0694	-0.035	0.0109	-0.0394	0.0861	0.0389	-0.0171	0.0914	0.0268	0.03	0.0325	0.0047	0.0614	28.579	-23.1986	41.4495
9	0.7153	-0.1779	-0.5271	0.1392	0.0164	0.626	-0.1123	0.0188	-0.1167	-0.0086	-0.0073	0.0769	0.1321	-0.0134	0.0222	0.0695	-0.0026	0.033	0.0571	-0.0208	0.1658	24.1612	-21.1173	65.3656
10	0.4146	0.0838	0.0981	0.3887	-0.2142	0.4446	0.0046	0.0746	-0.1012	-0.0018	0.0335	0.0376	0.1484	0.1742	-0.0163	0.0994	0.0479	0.0273	0.1127	-0.0093	0.1129	-14.9779	-20.9198	64.2904
11	0.6193	-0.2831	-0.1631	0.5037	-0.1341	0.7901	0.0127	-0.0186	-0.1407	0.0391	-0.032	0.1467	0.2311	-0.1685	0.0025	0.1768	-0.0467	0.033	0.131	0.0096	0.0748	-28.0145	-23.5188	79.1846
12	0.1202	0.0359	0.1157	0.0673	-0.0414	0.2124	-0.0021	-0.0548	-0.0506	0.0337	-0.0191	0.026	0.1162	-0.0173	0.0224	0.0945	0.0126	0.0522	0.0869	0.0146	0.128	-34.3269	-22.0241	50.0157
13	0.7856	-0.0168	0.2152	0.8663	-0.1396	0.5308	0.0177	0.0242	-0.0557	-0.017	0.0357	-0.0825	-0.088	0.0274	-0.0301	0.0498	0.0024	0.0474	0.0777	-0.005	0.0956	-12.1309	-10.8705	22.8855
14	0.1188	0.1539	-0.1629	0.2081	-0.2512	0.7374	0.0526	0.0178	0.1745	-0.0755	0.0374	0.0786	-0.0545	-0.0656	-0.0299	0.1835	-0.02	0.0765	0.0911	-0.0051	0.1699	-20.4097	7.7033	25.5701
15	0.5576	0.2762	0.3259	0.6567	-0.2502	0.6723	-0.043	0.0198	0.0828	0.0224	0.049	0.1606	-0.0778	-0.1686	0.0003	0.1759	0.0234	0.0531	0.1121	0.0222	0.1017	-27.1433	-2.2021	8.5736
16	0.2439	-0.0085	-0.3135	0.0136	0.0475	0.4998	0.0333	0.0621	0.1132	-0.0446	-0.0073	-0.0098	-0.0598	-0.0802	-0.0173	0.1019	0.0195	0.0557	0.1142	0.0273	0.1544	-33.3113	-3.784	28.6172
17	0.3627	-0.0591	0.2126	0.1957	-0.0607	0.5523	-0.0305	0.0476	0.0667	-0.0011	-0.0363	0.0142	0.0475	0.0313	0.0734	0.0794	0.0148	0.05	0.0866	0.0152	0.0911	-35.8077	-4.6384	46.1122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:78)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 79:180)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 181:258)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 259:383)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 384:493)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 2:168)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 169:245)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 246:439)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 440:496)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 3:117)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 118:273)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 274:494)
13	X-RAY DIFFRACTION	13	chain 'D' and (resseq 1:78)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 79:117)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 118:273)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 274:384)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 385:493)

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