PDB-6bqe: Low-resolution structure of cyclohexadienyl dehydratase from Pseu...

ID or keywords:

Entry

Database: PDB / ID: 6bqe

Title

Low-resolution structure of cyclohexadienyl dehydratase from Pseudomonas aeruginosa in space group P4322.

Components

Arogenate dehydratase

Keywords

LYASE / phenylalanine biosynthesis / cyclohexadienyl dehydratase / periplasmic binding protein

Function / homology

Function and homology information

arogenate dehydratase / arogenate dehydratase activity / prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process / periplasmic space
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Clifton, B.E. / Carr, P.D. / Jackson, C.J.

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.
Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Gerth, M.L. / Tokuriki, N. / Jackson, C.J.

History

Deposition	Nov 27, 2017	Deposition site: RCSB / Processing site: RCSB
Supersession	Dec 13, 2017	ID: 5JOT
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 30, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6bqe.cif.gz	288.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6bqe.ent.gz	245.3 KB	Display	PDB format
PDBx/mmJSON format	6bqe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6bqe_validation.pdf.gz	460 KB	Display	wwPDB validaton report
Full document	6bqe_full_validation.pdf.gz	464.8 KB	Display
Data in XML	6bqe_validation.xml.gz	25.9 KB	Display
Data in CIF	6bqe_validation.cif.gz	35 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/6bqe ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bqe	HTTPS FTP

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Related structure data

Related structure data	5tujC 5wjpC C: citing same article (ref.)
Similar structure data	5hpq-1 3c6m-1 2dg1-7 1brt-1 3c6k-2 4wqo-d 4iox-d 1jcm-2 3fob-d 1kkl-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: Arogenate dehydratase

B: Arogenate dehydratase

C: Arogenate dehydratase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	95.708, 95.708, 187.530
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

#1: Protein	Arogenate dehydratase Mass: 29349.311 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CF343_05215 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A232A1P4, UniProt: Q01269*PLUS
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.43 Å³/Da / Density % sol: 49 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: PEG 3350, 0.2 M ammonium acetate, 0.1 M TRIS pH 8.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 9, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 3.2→46.88 Å / Num. obs: 15009 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC_1/2: 0.944 / R_merge(I) obs: 0.339 / R_pim(I) all: 0.224 / Net I/σ(I): 5
Reflection shell	Resolution: 3.2→3.42 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.764 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2652 / CC_1/2: 0.59 / R_pim(I) all: 0.516 / R_rim(I) all: 0.926 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→41.729 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / Phase error: 27.41

	R_factor	Num. reflection	% reflection
R_free	0.2881	781	5.22 %
R_work	0.2366	-	-
obs	0.2393	14967	99.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.2→41.729 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5677	0	12	12	5701

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5824
X-RAY DIFFRACTION	f_angle_d	1.405	7910
X-RAY DIFFRACTION	f_dihedral_angle_d	16.248	2124
X-RAY DIFFRACTION	f_chiral_restr	0.068	864
X-RAY DIFFRACTION	f_plane_restr	0.007	1045

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 (%)
3.2-3.4005	0.3808	126	0.2976	2314	X-RAY DIFFRACTION	100
3.4005-3.6629	0.3228	120	0.2679	2324	X-RAY DIFFRACTION	100
3.6629-4.0312	0.3041	118	0.2471	2338	X-RAY DIFFRACTION	100
4.0312-4.6139	0.2704	160	0.2271	2327	X-RAY DIFFRACTION	100
4.6139-5.8105	0.2886	127	0.2144	2394	X-RAY DIFFRACTION	100
5.8105-41.7323	0.2237	130	0.2005	2489	X-RAY DIFFRACTION	98

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	0.8568	-0.0761	0.1451	0.3726	-0.0846	0.0723	0.0319	-0.3978	0.2579	0.3839	0.0589	-0.2669	0.2759	-0.0381	0.1691	0.4523	0.1111	-0.0508	0.398	0.0158	0.3073	22.8272	53.4453	22.9972
2	0.8833	-0.1026	0.2091	0.7826	-0.4279	0.5727	-0.0903	0.3404	0.1566	0.1922	0.0746	-0.2052	0.4172	0.2683	-0.007	0.3465	-0.0922	-0.0199	0.2465	-0.0248	0.2994	28.327	60.9832	19.939
3	0.3376	0.0691	-0.0492	0.7127	-0.2648	0.5888	-0.0647	0.1294	0.0949	0.2709	0.0817	-0.0052	-0.3412	0.1709	0.4499	0.3195	-0.0074	-0.0328	0.4084	0.0232	0.246	16.5311	64.3926	11.8843
4	0.1582	-0.1769	-0.2835	0.1917	-0.0374	1.7859	-0.1711	-0.0829	0.5649	-0.3222	0.15	-0.1408	-0.2478	0.7604	0.0403	0.394	-0.0672	0.0457	0.3036	-0.0587	0.4195	11.4037	78.6446	9.7082
5	1.3164	-1.2687	1.1667	2.0365	-0.8543	1.1384	-0.5	0.1015	0.3286	0.1663	0.0919	-0.4692	-0.107	-0.0254	-0.5685	0.2131	-0.0264	0.0806	0.3245	-0.0926	0.2822	9.8912	75.1532	19.6967
6	0.0674	0.0402	-0.0179	0.1757	0.1157	0.1601	-0.1018	0.0095	0.0959	0.1179	0.2552	0.0484	0.329	-0.2077	0.2716	0.3015	0.0364	0.0509	0.4878	0.0038	0.3316	10.6647	64.2443	11.9912
7	0.1341	-0.1122	0.1531	0.7197	-0.2089	0.2256	0.1678	-0.2781	0.0018	-0.2674	0.0706	-0.0502	-0.11	0.1425	0.6697	0.1812	-0.024	0.0517	0.323	-0.0132	0.3221	13.4279	51.1355	18.3649
8	0.198	0.0125	-0.0642	0.1514	-0.2256	0.2673	-0.0466	-0.0542	0.1553	0.1399	0.0828	0.0544	-0.3555	-0.0009	0.2833	0.1924	-0.0085	0.068	0.3109	-0.0233	0.3408	26.6291	61.3043	-15.5272
9	0.2755	0.2251	0.0216	0.211	0.0382	0.0142	-0.1614	0.216	0.6238	-0.1912	-0.1243	0.413	0.2892	0.1649	-0.0064	0.3647	0.0755	0.0211	0.4298	-0.0382	0.317	20.5996	66.3308	-16.2767
10	0.343	-0.0068	-0.1307	0.2	-0.1513	0.1097	0.0421	-0.1036	0.0462	-0.0576	0.052	-0.1245	0.1419	0.138	0.0201	0.2416	0.0195	0.02	0.2782	0.0503	0.247	27.1047	52.5939	-16.5255
11	0.1419	-0.1375	-0.1233	0.1406	0.1253	0.106	0.1282	-0.0039	-0.0896	0.0044	0.1693	0.0395	0.2553	0.2817	0.2042	0.2042	-0.0801	-0.0793	0.4143	-0.1223	0.2267	4.3078	46.0359	-28.9849
12	0.3881	-0.0523	0.4278	0.033	-0.1482	0.7052	-0.1338	0.2297	0.3013	-0.0398	0.0793	-0.0496	0.1468	0.2652	-0.0687	0.2791	-0.023	0.052	0.1691	-0.0707	0.4105	13.0275	39.6725	-31.2757
13	0.5077	-0.2332	0.504	0.3264	-0.8085	2.0472	-0.3278	0.4023	-0.0115	0.0898	0.1505	-0.0117	-0.3926	-0.0631	-0.6349	0.3316	-0.0753	0.0335	0.5124	0.0115	0.3148	11.7913	49.7968	-33.4414
14	0.0091	-0	-0.0316	0.4858	0.3479	0.5315	0.0126	0.1576	-0.0474	0.0827	-0.1668	0.2629	0.7873	0.0323	-0.3296	0.2599	-0.1112	0.0978	0.5022	0.0421	0.3249	11.8644	48.9228	-20.0743
15	0.0755	-0.0228	0.0405	-0.0084	0.0038	0.0215	0.0669	-0.3784	-0.1768	0.0846	0.0741	0.0437	0.0632	-0.0891	0.1258	0.2031	0.1619	0.088	0.5102	0.0046	0.3993	20.3769	57.2112	-2.5634
16	0.4573	0.0971	-0.8626	0.2095	-0.0132	2.2487	-0.3648	-0.0846	-0.1055	-0.0746	-0.1591	0.0595	-0.0136	0.1542	-0.6792	0.2305	-0.2104	0.0761	-0.0512	-0.1429	0.3014	9.3276	64.3913	-20.066
17	0.3824	-0.0541	0.0501	1.2599	-0.5759	0.2638	-0.2529	0.0044	-0.0917	-0.5118	-0.0315	-0.4291	0.1266	-0.149	-0.1503	0.4672	-0.0286	0.0477	0.3805	-0.0534	0.2939	26.7108	26.3489	-3.447
18	0.4335	0.1984	-0.0868	0.1883	-0.0131	0.057	-0.132	0.037	-0.3725	-0.2265	0.3833	-0.1648	0.2167	-0.1292	0.2806	0.5105	0.082	0.018	0.3263	0.0988	0.4038	24.596	23.9289	-2.6399
19	0.2533	-0.2135	0.1247	0.264	-0.1165	0.6998	-0.1061	0.1334	-0.1233	0.0569	-0.1392	-0.0457	-0.0413	0.047	-0.9858	0.3336	-0.0731	0.31	0.1495	-0.0938	0.2748	26.7128	28.8337	3.6949
20	0.1716	-0.0928	0.4529	0.1145	-0.2829	1.2636	-0.166	-0.0054	-0.0232	0.0528	-0.1421	0.0324	-0.5688	0.185	-0.1712	0.4087	0.1054	0.0467	0.3563	0.07	0.2306	23.4373	36.333	7.9821
21	0.4159	-0.2702	-0.7857	0.1783	0.5151	1.8213	0.1464	-0.1336	-0.3674	-0.0126	0.5166	0.3391	-0.3419	-0.2712	0.5357	0.3768	0.038	-0.1567	0.5982	0.0916	0.5549	1.6852	23.2273	13.9525
22	0.1224	-0.0113	-0.0419	0.2097	-0.02	0.0465	-0.3524	-0.0603	-0.2321	0.3947	-0.0315	0.089	0.6986	-0.1305	-0.0835	0.4895	-0.0209	0.1496	0.53	0.0884	0.6191	2.0838	24.3514	25.5034
23	0.5329	-0.037	0.4563	0.0042	-0.0308	0.4066	0.2389	0.4219	-0.028	-0.254	0.0698	0.0673	0.0894	0.3028	0.2771	0.1292	0.1052	0.0689	0.3423	0.0525	0.412	14.9385	23.5511	18.8438
24	0.5083	-0.2453	-0.2178	0.5415	-0.4271	2.0327	0.1446	0.0186	-0.1303	-0.3535	0.1248	0.2482	-0.0997	-0.6816	0.1239	0.4402	0.0532	-0.0419	0.2425	0.0091	0.4826	9.0172	16.9604	14.0385
25	0.8158	0.1085	0.3269	0.3509	0.3649	0.5656	-0.0295	0.1953	0.0335	0.1114	0.2434	0.1956	0.0396	0.0101	1.12	0.27	0.0077	0.0357	0.2066	0.1049	0.3678	15.0039	33.5859	1.8995
26	0.3282	0.0111	-0.5621	0.0085	0.0135	1.0116	0.3	-0.0899	-0.3191	-0.132	0.0877	0.009	0.0311	-0.9192	0.2523	0.6156	-0.1971	-0.1378	0.5174	0.023	0.3738	9.0585	21.9142	-5.0624

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 60 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 61 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 123 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 124 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 191 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 192 through 216 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 217 through 252 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 13 through 39 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 60 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 61 through 106 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 107 through 123 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 124 through 151 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 152 through 191 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 192 through 216 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 217 through 233 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 234 through 252 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 13 through 39 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 40 through 79 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 80 through 93 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 94 through 106 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 107 through 123 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 124 through 134 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 135 through 151 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 152 through 191 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 192 through 233 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 234 through 252 )

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