PDB-4ee6: Crystal Structure of the Novel Phenazine Prenyltransferase EpzP (...

ID or keywords:

Entry

Database: PDB / ID: 4ee6

Title

Crystal Structure of the Novel Phenazine Prenyltransferase EpzP (methylated)

Components

(Prenyltransferase

) x 2

Keywords

TRANSFERASE / PT fold / dihydrophenazine carboxylate prenyltransferase

Function / homology

Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase /

prenyltransferase activity /

metabolic process /

Prenyltransferase

Function and homology information

Biological species

Streptomyces cinnamonensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.33 Å

Authors

Zocher, G. / Stehle, T.

Citation

Journal: Plos One / Year: 2012
Title: Structure-based engineering increased the catalytic turnover rate of a novel phenazine prenyltransferase.
Authors: Zocher, G. / Saleh, O. / Heim, J.B. / Herbst, D.A. / Heide, L. / Stehle, T.

History

Deposition	Mar 28, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 14, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ee6.cif.gz	251.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ee6.ent.gz	213.4 KB	Display	PDB format
PDBx/mmJSON format	4ee6.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/ee/4ee6 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/4ee6	HTTPS FTP

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Related structure data

Related structure data	4ee7C 4ee8C C: citing same article (ref.)
Similar structure data	4ee7-2 7a77-d 2zvr-2 4ee7-1 5ekx-1 1zdw-d 5h6h-1 5y84-2 1a80-d 1zcw-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Prenyltransferase

B: Prenyltransferase

hetero molecules

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

1

A: Prenyltransferase

hetero molecules

defined by author&software
34 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Prenyltransferase

hetero molecules

defined by author&software
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	42.140, 135.600, 48.530
Angle α, β, γ (deg.)	90.00, 95.73, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 2 molecules AB

#1: Protein	Prenyltransferase / Mass: 33616.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cinnamonensis (bacteria) / Gene: epzP / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: E5KWG9
#2: Protein	Prenyltransferase / Mass: 33657.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cinnamonensis (bacteria) / Gene: epzP / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: E5KWG9

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Non-polymers , 4 types, 822 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.05 Å³/Da / Density % sol: 40.02 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 200 mM magnesium chloride, 30% (w/v) PEG4000, Tris hydrochloride ph 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 16, 2010
Radiation	Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.33→30 Å / Num. all: 123759 / Num. obs: 115868 / % possible obs: 93.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell	Resolution: 1.33→1.36 Å / % possible all: 63.7

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.33→29.93 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.938 / SU B: 1.879 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21313	3476	3 %	RANDOM
R_work	0.19019	-	-	-
obs	0.19088	112379	100 %	-
all	-	112379	-	-

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: 10.977 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	0 Å²	0.17 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	0.82 Å²

Refinement step

Cycle: LAST / Resolution: 1.33→29.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4485	0	39	804	5328

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4798
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3223
X-RAY DIFFRACTION	r_angle_refined_deg	1.41	1.988	6550
X-RAY DIFFRACTION	r_angle_other_deg	0.94	3	7887
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.925	5	622
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.202	23.622	196
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.005	15	686
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.894	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	738
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	5340
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	993
X-RAY DIFFRACTION	r_mcbond_it	0.934	5	2958
X-RAY DIFFRACTION	r_mcbond_other	0.463	5	1191
X-RAY DIFFRACTION	r_mcangle_it	1.162	5.5	4805
X-RAY DIFFRACTION	r_scbond_it	1.554	6	1840
X-RAY DIFFRACTION	r_scangle_it	1.952	6.5	1722

LS refinement shell

Resolution: 1.33→1.364 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	175	-
R_work	0.233	5649	-
obs	-	-	100 %

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	37.13	8.1267	-10.0999	9.3315	-4.6059	3.5132	0.222	0.1616	1.3235	-0.0885	0.6643	2.1329	-0.0073	-0.2823	-0.8863	0.0542	0.0028	-0.0219	0.5104	0.0372	0.5241	-6.213	-6.2111	-5.5684
2	10.4392	0.7871	2.7581	0.9292	-1.2059	3.0272	-0.0524	0.1635	-0.2781	-0.099	0.0642	-0.0584	0.1376	-0.0362	-0.0118	0.0659	-0.0118	0.008	0.0765	-0.0125	0.0096	6.1882	-7.6968	-1.7879
3	6.5907	0.3975	-1.2318	1.5156	0.2913	0.9157	-0.0123	0.2603	-0.3256	-0.0686	-0.0034	-0.0748	0.0425	-0.0444	0.0157	0.0685	-0.0176	-0.0025	0.0912	-0.0039	0.0207	-0.7579	-14.3212	2.625
4	12.6935	8.9828	-0.7338	16.1506	-0.3169	3.6418	-0.2449	0.1813	0.0519	-0.4013	0.2247	0.4303	-0.0724	-0.0826	0.0202	0.0457	0.0156	-0.0139	0.1121	0.0264	0.0225	-11.0037	-3.8106	3.8106
5	6.9404	-1.8457	0.5884	1.8174	-0.3377	0.1356	-0.1056	-0.2495	-0.0412	0.1859	0.1324	0.0097	0.0063	-0.0697	-0.0267	0.0689	-0.0044	-0.0047	0.0676	0.0129	0.012	5.1597	-5.2287	9.8925
6	0.2619	0.1886	-0.204	5.3436	-0.7951	0.2424	-0.0231	0.0457	-0.0061	-0.001	0.0248	0.069	0.0082	-0.0452	-0.0018	0.0585	-0.0022	-0.0131	0.0693	-0.0031	0.0169	-10.9456	-12.2494	14.4256
7	0.4838	-0.4296	-0.1652	1.0431	0.5302	0.9874	-0.0263	-0.0192	-0.0066	0.072	0.0429	-0.0627	0.0888	-0.0248	-0.0165	0.0465	-0.0066	-0.0143	0.0547	0.0044	0.0217	-5.7954	-8.732	20.2371
8	1.1488	0.1571	0.6251	0.8423	-0.3165	1.5962	0.0012	-0.0505	0.1015	0.0502	-0.0127	0.0653	-0.0587	0.0177	0.0116	0.0466	-0.0011	0.0047	0.0516	-0.006	0.0125	-1.5676	-1.0675	30.3755
9	1.773	-2.0948	0.0904	7.6709	0.672	1.3568	0.1171	0.0645	0.045	-0.2507	-0.132	-0.0942	0.1053	0.0302	0.0148	0.045	-0.0037	-0.0052	0.0788	-0.0059	0.0095	2.1061	-3.0057	24.0163
10	6.4097	-4.4778	1.7071	4.4044	-1.2533	2.2916	-0.044	-0.0632	0.3136	0.1543	0.04	-0.2357	-0.0961	0.1178	0.004	0.0649	-0.0163	-0.0051	0.047	-0.0079	0.0308	13.426	9.7973	30.7348
11	1.5974	-0.2236	0.2996	1.5028	-0.4274	1.8792	-0.0027	-0.0685	0.0678	0.0477	-0.0106	-0.0633	-0.0224	0.058	0.0134	0.0344	-0.0019	-0.0122	0.04	-0.0151	0.0203	18.7953	4.0408	25.831
12	0.907	1.6945	-1.2165	4.7071	-2.1312	1.6522	0.0026	-0.0175	0.0144	-0.0081	0.0148	0.0837	0.0097	0.0418	-0.0173	0.0348	0.0042	-0.0098	0.0579	-0.0023	0.005	8.1247	-3.459	26.6306
13	1.146	-0.1265	-0.1965	0.565	0.976	1.6883	0.005	0.1632	0.1964	-0.0373	0.0226	-0.0186	-0.0725	0.0509	-0.0276	0.066	-0.0178	-0.0078	0.0688	0.0231	0.0467	17.6488	5.1417	9.7444
14	2.8156	1.4563	0.0185	2.6862	2.0003	5.6285	0.0937	0.2557	0.2642	-0.1049	-0.0702	-0.124	-0.2323	0.1418	-0.0235	0.0735	-0.0095	0.0239	0.1126	0.0589	0.0887	12.3675	2.2506	0.6517
15	1.5845	-0.4362	1.2358	3.7801	-2.8382	5.2976	0.0069	0.017	-0.1045	-0.0421	0.0336	0.0467	-0.0081	0.006	-0.0405	0.0141	-0.0133	0.0076	0.0295	-0.0196	0.0208	12.9246	0.2199	16.7332
16	7.5609	-0.9677	6.2635	0.4114	-1.1287	6.5673	0.017	-0.1605	-0.0357	0.0143	0.0749	0.0783	0.0381	-0.1792	-0.0918	0.0388	-0.0074	0.0098	0.0429	0.0057	0.0225	8.3553	0.359	10.827
17	8.2115	-1.4251	-1.3017	2.3256	0.715	4.2859	-0.004	0.0042	0.029	0.0566	0.0813	-0.2601	0.103	0.3176	-0.0773	0.0799	-0.0007	-0.0157	0.0934	-0.0051	0.0328	20.7458	39.2053	-2.7146
18	8.6729	1.4577	-1.7387	8.3603	2.2951	6.4901	-0.0222	0.4707	0.2766	-0.3639	0.1097	0.2216	-0.0627	-0.0734	-0.0875	0.0581	-0.0022	-0.0161	0.0829	0.0216	0.0158	5.7657	40.7171	-0.252
19	7.2276	-1.4482	2.8012	1.4364	-1.4412	1.7702	-0.0567	0.2569	0.2793	-0.063	-0.0856	-0.1232	0.0103	0.1278	0.1423	0.101	-0.0077	0.0247	0.077	-0.0054	0.045	20.4556	45.5208	3.5973
20	5.1311	-1.4281	-0.6346	2.0209	0.1487	0.637	-0.0321	-0.1874	0.2367	0.0855	0.1121	-0.0948	-0.0264	0.0796	-0.0799	0.0609	-0.0075	-0.0077	0.0589	-0.0063	0.0185	10.816	37.4991	9.337
21	16.7267	-4.2158	6.7265	3.9093	1.2246	5.7023	0.1006	0.0613	-0.1572	-0.0098	-0.1502	0.1368	0.0627	-0.1191	0.0496	0.0649	0.0049	0.0288	0.0882	0.0015	0.0183	24.0978	33.7409	12.8826
22	0.5271	0.6608	-0.473	5.158	1.5956	5.6451	-0.0222	-0.0102	0.0437	-0.0133	0.0478	-0.036	-0.0267	0.1549	-0.0256	0.0265	-0.0129	-0.0114	0.043	-0.0053	0.0157	26.2696	47.4511	15.2284
23	0.5584	-0.6042	0.0573	1.0858	-0.5225	0.8985	-0.0297	-0.0112	-0.0226	0.0693	0.0696	0.0706	-0.0521	0.0087	-0.04	0.0434	-0.0046	0.0084	0.0503	-0.0032	0.021	21.7385	39.2866	20.5535
24	1.3137	-0.0812	-0.3566	1.7821	0.6442	1.5792	-0.034	-0.1584	-0.1091	0.1089	0.0527	-0.1724	0.0939	0.0886	-0.0187	0.0582	0.0043	-0.0154	0.0666	0.0064	0.0288	19.4036	32.9416	33.8003
25	13.7138	3.5604	-3.8507	2.3644	-1.5031	4.0827	-0.0682	-0.1127	-0.0083	0.1509	0.0635	-0.0623	0.1402	-0.2069	0.0046	0.0973	-0.0094	-0.014	0.0594	0.0166	0.0124	11.5821	25.8628	35.8702
26	0.9723	-0.0262	-0.1888	4.3704	-1.4298	1.5157	0.0352	0.0244	-0.0289	-0.0568	-0.0611	0.1553	-0.0987	-0.0482	0.0259	0.0445	0.0047	0.0023	0.0698	-0.0045	0.0172	15.5523	35.9353	23.7151
27	1.9783	-2.6093	-0.5231	4.3719	1.1233	1.0741	-0.0281	-0.1379	-0.1572	0.1159	0.0497	0.0857	0.0117	-0.0192	-0.0215	0.0591	-0.0118	0.0028	0.0595	0.0188	0.0333	2.2473	24.6843	31.8122
28	2.0497	-0.2269	-0.2423	1.2781	0.5058	1.6115	-0.0276	0.0104	-0.1315	0.0026	0.0029	-0.0027	0.0479	-0.0296	0.0248	0.0381	0.0007	-0.0011	0.0282	0.01	0.0137	-0.3267	26.3448	23.4933
29	1.1855	1.8925	1.1802	3.524	1.7355	1.2194	-0.0342	-0.0479	0.0283	-0.0609	-0.0123	-0.0118	-0.0405	-0.0666	0.0464	0.051	0.0094	0.0049	0.0568	-0.0023	0.0082	7.797	37.5834	27.9468
30	1.2292	-0.1029	-0.6527	0.7954	-1.0097	1.7879	-0.0398	0.1502	-0.201	-0.0483	0.0492	0.1089	0.0961	-0.1575	-0.0095	0.0576	-0.0115	-0.0031	0.0636	-0.0182	0.06	-1.5039	26.8037	9.9769
31	1.4439	1.0801	0.2458	4.1669	-1.4859	4.951	0.0091	0.3529	-0.1562	-0.2458	-0.0472	0.0832	0.0785	-0.0308	0.0382	0.093	-0.0016	-0.0204	0.1422	-0.0656	0.0355	5.1219	28.874	1.7748
32	2.559	-0.1846	-2.5928	0.6082	1.0117	4.6371	0.0279	0.0061	0.1318	-0.0312	0.0473	-0.0504	-0.0626	0.017	-0.0751	0.0415	-0.0022	-0.0085	0.0312	0.0017	0.0329	5.1882	32.4221	14.7138

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 9
2	X-RAY DIFFRACTION	2	A	10 - 21
3	X-RAY DIFFRACTION	3	A	22 - 37
4	X-RAY DIFFRACTION	4	A	38 - 43
5	X-RAY DIFFRACTION	5	A	44 - 65
6	X-RAY DIFFRACTION	6	A	66 - 85
7	X-RAY DIFFRACTION	7	A	86 - 117
8	X-RAY DIFFRACTION	8	A	118 - 167
9	X-RAY DIFFRACTION	9	A	168 - 180
10	X-RAY DIFFRACTION	10	A	181 - 195
11	X-RAY DIFFRACTION	11	A	196 - 216
12	X-RAY DIFFRACTION	12	A	217 - 238
13	X-RAY DIFFRACTION	13	A	239 - 253
14	X-RAY DIFFRACTION	14	A	254 - 266
15	X-RAY DIFFRACTION	15	A	267 - 279
16	X-RAY DIFFRACTION	16	A	280 - 290
17	X-RAY DIFFRACTION	17	B	1 - 14
18	X-RAY DIFFRACTION	18	B	15 - 23
19	X-RAY DIFFRACTION	19	B	24 - 40
20	X-RAY DIFFRACTION	20	B	41 - 61
21	X-RAY DIFFRACTION	21	B	62 - 70
22	X-RAY DIFFRACTION	22	B	71 - 85
23	X-RAY DIFFRACTION	23	B	86 - 122
24	X-RAY DIFFRACTION	24	B	123 - 150
25	X-RAY DIFFRACTION	25	B	151 - 158
26	X-RAY DIFFRACTION	26	B	159 - 180
27	X-RAY DIFFRACTION	27	B	181 - 201
28	X-RAY DIFFRACTION	28	B	202 - 221
29	X-RAY DIFFRACTION	29	B	222 - 238
30	X-RAY DIFFRACTION	30	B	239 - 253
31	X-RAY DIFFRACTION	31	B	254 - 268
32	X-RAY DIFFRACTION	32	B	269 - 291

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Protein , 2 types, 2 molecules AB

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Protein , 2 types, 2 molecules AB

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Non-polymers , 4 types, 822 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Yorodumi