PDB-6i5s: AH, Bottromycin amidohydrolase

ID or keywords:

Entry

Database: PDB / ID: 6i5s

Title

AH, Bottromycin amidohydrolase

Components

bottromycin amidohydrolase

Keywords

HYDROLASE / gatekeeper enzyme / bottromycin / amidohydrolase

Biological species

Streptomyces purpureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.73 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2019
Title: Thiazoline-Specific Amidohydrolase PurAH Is the Gatekeeper of Bottromycin Biosynthesis.
Authors: Sikandar, A. / Franz, L. / Melse, O. / Antes, I. / Koehnke, J.

History

Deposition	Nov 14, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2019	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6i5s.cif.gz	184.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6i5s.ent.gz	153.1 KB	Display	PDB format
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Validation report

Summary document	6i5s_validation.pdf.gz	437.4 KB	Display	wwPDB validaton report
Full document	6i5s_full_validation.pdf.gz	437.6 KB	Display
Data in XML	6i5s_validation.xml.gz	18.9 KB	Display
Data in CIF	6i5s_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/6i5s ftp://data.pdbj.org/pub/pdb/validation_reports/i5/6i5s	HTTPS FTP

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Related structure data

Similar structure data	5oua-d 5n1d-d 1cmk-d 4ptm-d 1e2s-d 5hue-d 3e8c-2 6v87-d 5aau-d 5m6y-d Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: bottromycin amidohydrolase

hetero molecules

51.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	100.973, 110.726, 84.896
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-792- HOH

#1: Protein	bottromycin amidohydrolase Mass: 50990.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: modified residue: KCX; lysine carboxylic acid / Source: (gene. exp.) Streptomyces purpureus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.33 Å³/Da / Density % sol: 47.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.0 - 4.2 M sodium formate

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID23-1	1	0.97242
SYNCHROTRON	ESRF	MASSIF-3	2	0.96775

Detector

Type	ID	Detector	Date
DECTRIS PILATUS3 6M	1	PIXEL	Apr 18, 2017
DECTRIS EIGER X 4M	2	PIXEL	Dec 9, 2016

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97242	1
2	0.96775	1

Reflection

Entry-ID: 6I5S

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Net I/σ(I)
1.73-56.04	48843	97.78	4.5	0.034	1	20.12
2.5-43.34	16768	99.8	92.7		2	55.7

Reflection shell

Resolution: 1.73→1.76 Å / R_merge(I) obs: 0.693

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.73→56.043 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1885	2383	4.88 %
R_work	0.158	-	-
obs	0.1595	48812	97.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.73→56.043 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3388	0	9	207	3604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	3502
X-RAY DIFFRACTION	f_angle_d	1.093	4786
X-RAY DIFFRACTION	f_dihedral_angle_d	14.945	2066
X-RAY DIFFRACTION	f_chiral_restr	0.07	523
X-RAY DIFFRACTION	f_plane_restr	0.009	638

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 (%)
1.73-1.7653	0.3418	133	0.3035	2759	X-RAY DIFFRACTION	99
1.7653-1.8037	0.3085	123	0.2749	2775	X-RAY DIFFRACTION	100
1.8037-1.8457	0.2763	145	0.2434	2712	X-RAY DIFFRACTION	99
1.8457-1.8918	0.2606	129	0.2248	2734	X-RAY DIFFRACTION	99
1.8918-1.943	0.2459	146	0.1969	2733	X-RAY DIFFRACTION	99
1.943-2.0002	0.2503	144	0.1819	2709	X-RAY DIFFRACTION	99
2.0002-2.0647	0.223	137	0.1667	2766	X-RAY DIFFRACTION	99
2.0647-2.1385	0.2405	143	0.1644	2755	X-RAY DIFFRACTION	99
2.1385-2.2241	0.204	142	0.1487	2725	X-RAY DIFFRACTION	99
2.2241-2.3254	0.1937	137	0.1465	2729	X-RAY DIFFRACTION	98
2.3254-2.448	0.1879	138	0.1417	2699	X-RAY DIFFRACTION	97
2.448-2.6013	0.1821	142	0.1506	2695	X-RAY DIFFRACTION	97
2.6013-2.8022	0.187	162	0.1593	2725	X-RAY DIFFRACTION	98
2.8022-3.0842	0.2248	138	0.1597	2727	X-RAY DIFFRACTION	97
3.0842-3.5304	0.1768	164	0.1453	2670	X-RAY DIFFRACTION	96
3.5304-4.4476	0.1505	125	0.126	2723	X-RAY DIFFRACTION	95
4.4476-56.0719	0.1545	135	0.1636	2793	X-RAY DIFFRACTION	94

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	1.9422	0.2664	-0.4844	1.1291	-0.1898	2.0072	0.0983	-0.0001	0.0374	-0.0896	0.0427	-0.0859	0.1744	0.1794	-0.1485	0.2595	0.0132	-0.0086	0.2178	-0.0598	0.2136	26.9141	1.2292	64.4254
2	0.4768	0.2067	0.1765	1.1936	-0.2962	1.9782	0.0469	0.0172	-0.0273	-0.0617	-0.0103	-0.0455	0.0784	0.1874	-0.0535	0.219	0.0176	0.0005	0.21	-0.0128	0.2136	29.68	6.1815	66.8767
3	1.1558	-0.3187	-1.0737	3.191	0.4222	1.6856	-0.0477	-0.1024	0.0064	0.2572	0.06	0.1783	-0.158	-0.0577	-0.0306	0.3155	0.0243	-0.0193	0.2743	-0.0061	0.2532	19.228	18.314	89.8849
4	1.6893	-0.5199	-0.0717	2.0595	-0.7402	2.057	0.1112	-0.0375	0.324	0.1487	0.0227	-0.0865	-0.4348	-0.1125	-0.1249	0.3635	-0.0025	0.0458	0.2432	-0.0246	0.2819	22.3292	31.8122	77.9897
5	2.496	1.517	0.2445	4.2204	0.9559	1.0551	-0.0815	0.4392	0.2572	-0.2214	0.05	0.4627	-0.0657	0.0157	0.0537	0.3007	0.0465	-0.0243	0.3506	0.0346	0.3327	13.2147	24.4886	60.0315
6	2.4127	-0.4414	0.3728	1.635	-0.165	1.5509	-0.0395	0.13	0.0791	-0.1552	0.0643	0.2243	-0.2877	-0.0987	-0.0424	0.3128	0.0043	0.0037	0.2363	0.0418	0.3069	14.9295	30.4827	64.3608
7	0.3636	0.4606	-0.4749	1.6987	0.6683	2.06	0.0397	-0.0151	0.0433	-0.0354	0.0243	-0.2039	0.053	0.2594	-0.0536	0.2502	0.005	0.0069	0.2625	0.0107	0.2489	30.3782	17.1811	66.665
8	2.2938	-0.5666	0.271	1.973	-0.1348	1.6379	0.091	0.3312	0.0652	-0.5253	-0.0759	0.004	-0.0341	0.0858	-0.0286	0.3733	0.0208	-0.0034	0.3477	-0.0049	0.2308	24.4436	9.3549	53.0999

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 147 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 216 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 217 through 272 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 273 through 297 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 298 through 339 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 340 through 405 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 406 through 460 )

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