PDB-4zu2: Pseudomonas aeruginosa AtuE

ID or keywords:

Entry

Database: PDB / ID: 4zu2

Title

Pseudomonas aeruginosa AtuE

Components

Putative isohexenylglutaconyl-CoA hydratase

Keywords

HYDROLASE / terpenes / crotonase

Function / homology

Function and homology information

terpene catabolic process / isoprenoid catabolic process / catalytic activity
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Poudel, N. / Pfannstiel, J. / Simon, O. / Walter, N. / Jendrossek, D. / Papageorgiou, A.C.

Citation

Journal: Appl.Environ.Microbiol. / Year: 2015
Title: The Pseudomonas aeruginosa Isohexenyl Glutaconyl Coenzyme A Hydratase (AtuE) Is Upregulated in Citronellate-Grown Cells and Belongs to the Crotonase Family.
Authors: Poudel, N. / Pfannstiel, J. / Simon, O. / Walter, N. / Papageorgiou, A.C. / Jendrossek, D.

History

Deposition	May 15, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2015	Group: Database references
Revision 1.2	Jul 17, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zu2.cif.gz	211.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4zu2.ent.gz	170.8 KB	Display	PDB format
PDBx/mmJSON format	4zu2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zu2_validation.pdf.gz	446.8 KB	Display	wwPDB validaton report
Full document	4zu2_full_validation.pdf.gz	460.2 KB	Display
Data in XML	4zu2_validation.xml.gz	34.4 KB	Display
Data in CIF	4zu2_validation.cif.gz	49.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/4zu2 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zu2	HTTPS FTP

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Related structure data

Related structure data	3h81S 3i47S S: Starting model for refinement
Similar structure data	3qxz-d 2vx2-3 4fjw-d 4q1k-d 3hrx-2 5ve2-2 1szo-3 3swx-d 3r9s-d 3pzk-d 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: Putative isohexenylglutaconyl-CoA hydratase

B: Putative isohexenylglutaconyl-CoA hydratase

C: Putative isohexenylglutaconyl-CoA hydratase

hetero molecules

87.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	108.440, 133.970, 83.350
Angle α, β, γ (deg.)	90.00, 139.46, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Putative isohexenylglutaconyl-CoA hydratase Mass: 28720.795 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: atuE, PA2890 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9HZV7
#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Formula: I
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.22 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium iodide, 20 % (v/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8123 Å / Relative weight: 1
Reflection	Resolution: 2.13→20 Å / Num. obs: 42012 / % possible obs: 95.8 % / Redundancy: 2 % / R_merge(I) obs: 0.114 / Net I/σ(I): 8.4
Reflection shell	Resolution: 2.13→2.25 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.2 / % possible all: 90.6

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3H81 and 3I47

3h81

3i47

Resolution: 2.15→19.693 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.257	2045	4.98 %
R_work	0.1976	-	-
obs	0.2006	41059	97.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→19.693 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5697	0	14	435	6146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	5760
X-RAY DIFFRACTION	f_angle_d	1.523	7791
X-RAY DIFFRACTION	f_dihedral_angle_d	16.155	2112
X-RAY DIFFRACTION	f_chiral_restr	0.082	912
X-RAY DIFFRACTION	f_plane_restr	0.007	1047

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 (%)
2.15-2.2	0.3326	133	0.307	2613	X-RAY DIFFRACTION	98
2.2-2.2549	0.3085	134	0.2809	2583	X-RAY DIFFRACTION	98
2.2549-2.3158	0.3388	136	0.283	2604	X-RAY DIFFRACTION	98
2.3158-2.3838	0.3198	135	0.2647	2595	X-RAY DIFFRACTION	99
2.3838-2.4606	0.3125	138	0.2375	2620	X-RAY DIFFRACTION	99
2.4606-2.5484	0.317	135	0.2333	2626	X-RAY DIFFRACTION	99
2.5484-2.6502	0.3408	137	0.2254	2579	X-RAY DIFFRACTION	98
2.6502-2.7705	0.3164	138	0.2182	2641	X-RAY DIFFRACTION	99
2.7705-2.9161	0.2581	138	0.2047	2607	X-RAY DIFFRACTION	99
2.9161-3.0982	0.29	139	0.2067	2621	X-RAY DIFFRACTION	99
3.0982-3.3363	0.2432	137	0.1884	2612	X-RAY DIFFRACTION	99
3.3363-3.6701	0.2501	138	0.1674	2605	X-RAY DIFFRACTION	98
3.6701-4.1967	0.208	137	0.1559	2600	X-RAY DIFFRACTION	98
4.1967-5.2706	0.2048	136	0.1614	2586	X-RAY DIFFRACTION	97
5.2706-19.6934	0.2489	134	0.21	2522	X-RAY DIFFRACTION	93

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	0.9821	-0.8376	0.6851	2.982	-0.6603	1.8003	-0.046	-0.2786	-0.2767	-0.1252	-0.0334	-0.5265	-0.0242	-0.8699	0.1932	0.2955	0.1862	0.136	1.0397	-0.1012	0.6394	67.1254	7.3379	27.8117
2	2.6798	-0.9334	-0.237	3.0608	0.0747	3.4425	0.1948	0.7547	-0.1382	0.482	-0.4417	-0.7251	0.4212	0.1976	0.1602	0.3208	0.0642	-0.0275	0.9078	-0.02	0.479	64.6067	3.5498	23.0284
3	3.0621	1.2518	0.0669	2.7397	-1.4624	2.1662	-0.046	0.0206	-0.0528	0.0602	-0.0131	-0.5142	0.0128	0.9844	0.1812	0.3308	0.0206	-0.091	0.794	-0.0376	0.3303	57.3248	6.1674	31.6775
4	2.0038	-0.1198	0.0683	1.599	-0.3079	2.8854	0.0884	0.7987	-0.0749	-0.2757	-0.6803	-0.5107	0.1607	0.7899	-0.7567	0.3437	0.1063	0.1315	0.9834	0.0224	0.4029	62.0234	8.1655	20.5411
5	8.5336	-2.1801	2.99	2.6779	1.0822	4.1643	0.0066	-0.6875	-0.6432	0.1579	0.5851	-0.5313	1.3161	0.3409	0.4443	0.7121	0.206	0.1177	0.8117	-0.1387	0.3344	57.3072	-5.0111	20.7616
6	2.7696	1.5704	1.8357	1.4126	1.0596	2.545	0.0319	0.7881	0.6715	-1.3089	0.1604	-0.8948	0.1074	1.0358	-0.14	0.774	0.2344	0.0097	0.5978	-0.0011	0.8787	54.4913	-16.2382	29.8546
7	3.9093	1.1679	2.9169	2.0015	3.4572	2.7613	-0.1011	-1.6133	-0.6263	1.9095	-0.0314	0.1026	0.8655	-0.5215	-0.3766	0.6511	0.331	-0.0745	0.768	-0.028	0.3626	46.6761	-11.0235	34.6747
8	1.006	-0.1228	0.4154	1.8161	-1.0415	0.8651	-0.1949	-0.2002	0.2057	-0.0653	-0.0777	-0.4348	-0.1082	0.2834	0.2252	0.2481	0.0175	0.003	0.4801	-0.0008	0.186	50.1315	7.2129	27.5578
9	0.6164	-0.0599	-0.6095	1.2704	-1.7347	3.1492	0.4351	-0.6232	0.164	0.2119	-0.3216	0.0249	-0.5713	0.7504	-0.2146	0.3567	-0.0098	0.1996	1.0085	0.1041	0.589	60.1034	3.778	13.5093
10	2.3944	-0.8954	-1.4754	9.2859	0.6507	0.9188	-0.1254	-0.165	-0.3145	0.501	-0.0913	-0.857	0.2497	0.7748	-0.1772	0.2056	0.1453	0.1474	0.7665	-0.0091	0.1785	52.2432	3.9167	17.2319
11	1.1202	-0.5457	-0.0391	0.6497	0.8631	1.8314	0.1786	0.5291	0.2834	-0.3997	0.2986	-1.0165	0.306	0.6692	3.1982	0.1245	0.2271	0.272	0.6651	-0.1993	0.326	49.8222	-7.1495	13.9378
12	1.5573	2.2218	-0.7373	3.6506	-1.3725	0.565	-0.2885	0.077	0.1268	-0.1571	0.6213	0.0513	0.3922	-0.1538	0.2774	0.2715	0.0575	0.0451	0.2746	-0.088	0.1382	42.4505	-0.506	21.844
13	3.5869	0.7098	-0.0934	2.2761	-0.202	0.0192	-0.3231	0.2489	0.4006	0.2512	0.4436	0.0032	0.2698	0.72	0.0199	0.2502	0.1105	0.0119	0.4185	-0.1201	0.1585	40.2644	-0.9749	12.2673
14	0.9886	0.0173	0.0722	1.9594	0.6282	1.7668	-0.1452	0.6647	0.1765	-0.3151	0.1657	-0.1851	0.4409	0.4361	-0.1148	0.3245	0.0346	0.1233	0.774	0.046	0.3408	50.5936	4.8435	6.9366
15	1.7177	-1.4223	0.1505	1.3822	-0.3325	2.5997	0.0326	1.5287	0.8183	-0.7214	0.0439	-0.6907	-0.4725	1.1622	-0.0243	0.3363	-0.2143	0.0767	1.1327	0.1442	0.866	61.6522	17.1638	12.3064
16	0.9689	-1.0264	0.1427	1.8321	0.1738	2.3445	-0.1432	0.0752	0.8791	0.4062	-0.0161	-0.4285	-0.0905	0.3518	0.2908	0.3368	-0.0585	-0.0488	0.4555	0.0412	0.4776	46.2183	21.0787	25.5737
17	2.1572	-1.5635	0.1069	1.5456	-1.0977	2.5543	-0.295	-0.3521	-1.5946	0.4906	0.64	-0.5946	0.3022	-0.0572	-0.2081	0.4136	-0.109	-0.0632	0.4822	-0.0687	0.6833	32.6882	21.0919	27.2299
18	2.4497	0.4027	0.0944	3.1196	-0.2214	1.4893	-0.7875	-0.2587	0.0684	1.1814	-0.0139	-0.0628	0.1204	0.5514	0.1771	0.7793	-0.1606	-0.0187	0.3837	-0.0522	0.5424	40.9997	30.9065	30.7462
19	3.0483	0.4855	-3.8402	0.5818	-0.8438	4.94	0.2033	0.4904	0.9685	0.6594	0.8664	-0.7472	-1.1227	0.9793	-0.1008	0.6294	-0.0494	-0.2693	0.5021	-0.0882	0.8808	50.7122	35.7793	27.4784
20	1.896	-1.2197	0.4048	1.7049	0.1851	0.624	0.2371	0.5436	1.2184	-1.0756	0.3552	-0.717	-0.7238	0.9541	-0.1116	0.6829	-0.3151	0.0184	0.7465	0.0348	0.9121	57.6346	37.1204	20.1942

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain C and resid 7:14)
2	X-RAY DIFFRACTION	2	(chain C and resid 15:28)
3	X-RAY DIFFRACTION	3	(chain C and resid 29:51)
4	X-RAY DIFFRACTION	4	(chain C and resid 52:63)
5	X-RAY DIFFRACTION	5	(chain C and resid 64:69)
6	X-RAY DIFFRACTION	6	(chain C and resid 70:78)
7	X-RAY DIFFRACTION	7	(chain C and resid 79:88)
8	X-RAY DIFFRACTION	8	(chain C and resid 89:107)
9	X-RAY DIFFRACTION	9	(chain C and resid 108:111)
10	X-RAY DIFFRACTION	10	(chain C and resid 112:129)
11	X-RAY DIFFRACTION	11	(chain C and resid 130:145)
12	X-RAY DIFFRACTION	12	(chain C and resid 146:154)
13	X-RAY DIFFRACTION	13	(chain C and resid 155:170)
14	X-RAY DIFFRACTION	14	(chain C and resid 171:187)
15	X-RAY DIFFRACTION	15	(chain C and resid 188:206)
16	X-RAY DIFFRACTION	16	(chain C and resid 207:222)
17	X-RAY DIFFRACTION	17	(chain C and resid 223:235)
18	X-RAY DIFFRACTION	18	(chain C and resid 236:241)
19	X-RAY DIFFRACTION	19	(chain C and resid 242:251)
20	X-RAY DIFFRACTION	20	(chain C and resid 252:264)

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