PDB-5z43: Crystal structure of prenyltransferase AmbP1 apo structure

ID or keywords:

Entry

Database: PDB / ID: 5z43

Title

Crystal structure of prenyltransferase AmbP1 apo structure

Components

AmbP1

Keywords

TRANSFERASE / Prenyltransferase / AmbP1 / indole

Function / homology

Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / AmbP1

Function and homology information

Biological species

Fischerella ambigua UTEX 1903 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.361 Å

Authors

Awakawa, T. / Nakashima, Y. / Mori, T. / Abe, I.

Citation

Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Molecular Insight into the Mg2+-Dependent Allosteric Control of Indole Prenylation by Aromatic Prenyltransferase AmbP1
Authors: Awakawa, T. / Mori, T. / Nakashima, Y. / Zhai, R. / Wong, C.P. / Hillwig, M.L. / Liu, X. / Abe, I.

History

Deposition	Jan 10, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 6, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 2023	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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PDBx/mmCIF format	5z43.cif.gz	251.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z4/5z43 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z43	HTTPS FTP

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Related structure data

Related structure data	5yk9SC 5z44C 5z45C 5z46C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5z46-1 5yk9-1 5z44-2 5yk9-2 5z45-2 4gga-d 5ynu-1 5d8w-1 5z46-2 1zb6-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: AmbP1

B: AmbP1

hetero molecules

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

1

A: AmbP1

hetero molecules

defined by author&software
Evidence: gel filtration
35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AmbP1

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.263, 116.263, 48.723
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	AmbP1 / Aromatic prenyltransferase / Orf2-1-related aromatic prenyltransferase Mass: 35154.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria) Gene: ambP1, famD2 / Production host: Escherichia coli (E. coli) / References: UniProt: V5TDZ4
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.34 Å³/Da / Density % sol: 47.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM MES (pH6.5), 0.2M MgCl2, 22% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.36→44.9 Å / Num. obs: 27028 / % possible obs: 99.6 % / Redundancy: 3.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.038 / Net I/σ(I): 18.8
Reflection shell	Resolution: 2.36→2.45 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.493 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2823 / CC_1/2: 0.807 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5YK9

5yk9

Resolution: 2.361→41.105 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1

	R_factor	Num. reflection	% reflection
R_free	0.24	1987	7.36 %
R_work	0.1902	-	-
obs	0.1939	27011	99.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.361→41.105 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4687	0	2	83	4772

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4818
X-RAY DIFFRACTION	f_angle_d	0.973	6548
X-RAY DIFFRACTION	f_dihedral_angle_d	20.676	1753
X-RAY DIFFRACTION	f_chiral_restr	0.054	701
X-RAY DIFFRACTION	f_plane_restr	0.006	860

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 (%)
2.3606-2.4196	0.3157	143	0.2509	1803	X-RAY DIFFRACTION	100
2.4196-2.485	0.2914	141	0.2411	1739	X-RAY DIFFRACTION	99
2.485-2.5582	0.3254	138	0.2379	1782	X-RAY DIFFRACTION	100
2.5582-2.6407	0.3374	139	0.2349	1762	X-RAY DIFFRACTION	100
2.6407-2.7351	0.3176	140	0.2233	1773	X-RAY DIFFRACTION	100
2.7351-2.8446	0.2584	142	0.2118	1780	X-RAY DIFFRACTION	100
2.8446-2.974	0.2822	144	0.211	1784	X-RAY DIFFRACTION	100
2.974-3.1307	0.2724	141	0.2009	1770	X-RAY DIFFRACTION	100
3.1307-3.3268	0.2811	144	0.197	1795	X-RAY DIFFRACTION	100
3.3268-3.5835	0.2437	142	0.1795	1795	X-RAY DIFFRACTION	100
3.5835-3.9439	0.236	142	0.1793	1794	X-RAY DIFFRACTION	99
3.9439-4.514	0.2145	141	0.1703	1783	X-RAY DIFFRACTION	99
4.514-5.6847	0.1907	142	0.1751	1813	X-RAY DIFFRACTION	99
5.6847-41.1114	0.2101	148	0.1829	1851	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	7.4888	-2.2058	1.5884	9.3409	-5.3848	9.2154	-0.2344	-0.0317	0.566	-0.4523	0.1927	-0.1326	-0.652	0.791	0.0958	0.5997	-0.2604	-0.2077	0.8949	0.2046	0.7198	48.3239	16.7353	4.7755
2	6.9816	-0.4455	-1.2641	5.5772	-0.1781	7.406	-0.5607	-0.1657	-0.2192	-0.1455	0.0051	-0.5756	-0.1681	0.5551	0.459	0.4594	-0.1685	-0.1265	0.6425	0.2463	0.6342	40.5787	11.7432	1.4488
3	8.0448	2.7412	-1.2458	4.8242	-1.1737	2.9582	-0.624	1.3562	0.4871	-0.3392	0.4156	-0.3813	-0.4806	0.1123	0.2722	0.6386	-0.1767	-0.0828	0.7196	0.2386	0.5012	28.1919	15.636	-12.2066
4	2.3408	-0.3102	0.5697	0.3195	-0.5054	2.7115	-0.3196	-0.1767	0.1413	-0.2975	0.2207	-0.0695	-0.4098	0.2227	0.3219	0.599	-0.1379	-0.0954	0.4766	0.1777	0.7476	29.4602	13.8202	-3.6
5	2.5136	-0.3657	0.2281	2.6001	0.4929	5.1143	-0.1798	0.1993	0.2999	-0.2793	-0.0446	0.0633	-0.3442	-0.0319	0.2117	0.3363	-0.0343	-0.0561	0.3182	0.0839	0.4265	14.45	6.045	2.6405
6	3.5856	1.2665	1.631	6.3554	3.1204	3.3575	-0.1356	-0.4967	-0.03	0.5086	0.1391	0.2266	0.1518	0.0614	0.0272	0.3353	-0.0265	0.0238	0.4297	0.0856	0.4102	20.5998	2.8284	12.975
7	3.973	0.5963	1.0875	3.9156	-0.452	3.283	-0.1476	-0.1046	-0.0111	0.5198	0.003	-0.5751	-0.3513	0.9583	0.1154	0.4159	-0.0215	-0.0548	0.533	0.1103	0.417	27.4348	5.1873	11.6847
8	6.4269	2.037	-0.3661	4.6805	-1.7301	4.271	-0.0567	-0.7151	-0.6448	0.7903	-0.061	-0.4018	-0.2887	0.8332	0.0427	0.4536	0.0427	-0.0611	0.6495	0.1887	0.5168	35.0127	6.9858	14.1102
9	7.2355	-0.6574	-2.8632	0.6643	-0.2044	4.8439	0.1303	-0.7181	1.3435	0.4229	-0.1806	-0.4289	-0.898	0.1354	0.0586	0.5462	-0.059	-0.1744	0.489	0.0438	0.6856	31.9293	16.7418	11.0543
10	4.3465	0.8959	-0.6872	2.7235	-0.7564	6.6954	0.6077	-0.2071	-1.4548	0.2817	0.0488	-0.9507	2.1983	-0.0585	-0.5735	1.5087	0.0367	-0.407	0.5559	0.0995	1.1755	66.3316	10.0757	26.9012
11	2.3591	3.037	-2.666	7.7966	-0.3647	9.484	0.1117	-0.7038	-0.4234	-0.4531	0.3966	0.3293	1.7415	0.057	-0.6651	0.92	-0.0117	-0.3715	0.48	0.1446	0.7769	63.4428	19.4641	23.1465
12	0.992	-0.6438	0.2706	4.5377	-1.0009	4.0954	0.3023	-0.7505	-0.8844	0.8336	0.2755	0.2198	0.6544	-0.5369	-0.5983	0.7899	-0.1619	-0.1508	0.7166	0.3161	0.8179	56.6198	27.4935	35.1287
13	4.6553	0.5966	0.9188	3.9438	-1.073	7.5499	0.0942	-0.3048	-0.1092	0.1033	0.1855	-0.0007	0.1922	-0.335	-0.2678	0.2379	0.014	-0.0353	0.2321	0.0058	0.2779	59.9574	42.8245	23.3826
14	5.4918	1.6792	-1.0608	6.5775	1.7661	4.0372	-0.0131	0.4503	-0.5237	-0.4794	0.1644	-0.354	0.5059	0.4799	-0.1166	0.3619	0.0528	0.0129	0.3561	-0.0047	0.3731	66.4005	39.321	16.8048
15	4.1211	0.7923	0.3588	10.0259	2.275	5.9014	0.3567	0.8906	-0.9309	-0.4454	0.3802	-0.3249	1.5064	0.3124	-0.9121	0.6869	0.0229	-0.1821	0.5873	-0.0748	0.5158	64.4181	28.3135	11.3972
16	3.1933	-1.2385	-0.3197	8.5908	-1.9445	6.3015	0.7187	0.7558	-0.9272	-0.846	0.0889	-1.0304	1.9083	0.1463	-0.6881	0.8982	0.1268	-0.2942	0.4818	-0.1451	0.7332	67.2185	23.2791	13.0684
17	2.3615	-0.9688	1.9166	6.505	2.0886	4.5965	0.9183	-1.1916	-0.8758	-0.0506	-0.7489	0.9753	1.1993	-1.1803	-0.1084	0.9369	-0.1762	-0.4195	0.7073	0.0901	0.9569	58.6184	21.2878	16.5745

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 122 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 123 through 191 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 192 through 215 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 216 through 242 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 243 through 275 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 276 through 292 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 34 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 35 through 63 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 64 through 127 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 128 through 190 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 191 through 220 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 221 through 242 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 243 through 275 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 276 through 290 )

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