PDB-3skv: Salicylyl-Acyltransferase SsfX3 from a Tetracycline Biosynthetic ...

ID or keywords:

Entry

Database: PDB / ID: 3skv

Title

Salicylyl-Acyltransferase SsfX3 from a Tetracycline Biosynthetic Pathway

Components

SsfX3

Keywords

TRANSFERASE / jelly roll / GDSL/SGNH fold / alpha/beta hydrolase fold

Function / homology

Function and homology information

: / SsfX3, N-terminal domain / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Jelly Rolls / Sandwich / Rossmann fold ...
Similarity search - Domain/homology

Biological species

Streptomyces sp. SF2575 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.49 Å

Authors

Pickens, L.B. / Sawaya, M.R. / Yeates, T.O. / Tang, Y.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structural and Biochemical Characterization of the Salicylyl-acyltranferase SsfX3 from a Tetracycline Biosynthetic Pathway.
Authors: Pickens, L.B. / Sawaya, M.R. / Rasool, H. / Pashkov, I. / Yeates, T.O. / Tang, Y.

History

Deposition	Jun 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2011	Group: Database references
Revision 1.2	Dec 21, 2011	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3skv.cif.gz	280.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3skv.ent.gz	226.3 KB	Display	PDB format
PDBx/mmJSON format	3skv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3skv_validation.pdf.gz	452.3 KB	Display	wwPDB validaton report
Full document	3skv_full_validation.pdf.gz	461 KB	Display
Data in XML	3skv_validation.xml.gz	26.7 KB	Display
Data in CIF	3skv_validation.cif.gz	37.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/3skv ftp://data.pdbj.org/pub/pdb/validation_reports/sk/3skv	HTTPS FTP

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Related structure data

Similar structure data	6ydb-1 4w8l-2 1k4l-1 5dov-2 1lq1-2 1k4i-1 6azv-3 6c5q-d 6wrk-d 4pbt-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SsfX3

B: SsfX3

hetero molecules

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

1

A: SsfX3

hetero molecules

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

2

B: SsfX3

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	66.211, 84.394, 127.943
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	SsfX3 Mass: 42528.984 Da / Num. of mol.: 2 / Mutation: C68H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SF2575 (bacteria) / Gene: ssfX3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D6MSV6, Transferases; Acyltransferases
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.1 Å³/Da / Density % sol: 41.46 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.3 M sodium formate, pH 7.0, 0.01 M L-glutathione reduced, 0.01 M L-glutathione oxidized, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 0.9791, 0.9794, 0.9715

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2009

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9791	1
2	0.9794	1
3	0.9715	1

Reflection

Resolution: 2.49→28.801 Å / Num. all: 25713 / Num. obs: 25713 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / R_merge(I) obs: 0.068 / Χ²: 1.15 / Net I/σ(I): 9.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.5-2.59	4.8	0.549	2488	1.142	1	100
2.59-2.69	4.8	0.419	2553	1.121	1	99.9
2.69-2.82	4.8	0.313	2533	1.196	1	100
2.82-2.96	4.8	0.232	2529	1.196	1	100
2.96-3.15	4.8	0.166	2573	1.159	1	99.9
3.15-3.39	4.7	0.114	2548	1.175	1	99.9
3.39-3.73	4.6	0.081	2564	1.106	1	99.9
3.73-4.27	4.4	0.063	2570	1.075	1	99.1
4.27-5.39	4.2	0.048	2598	1.156	1	98.9
5.39-150	4.3	0.03	2757	1.165	1	99.6

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.5 Å / D res low: 19.98 Å / FOM : 0.317 / FOM acentric: 0.31 / FOM centric: 0.365 / Reflection: 15264 / Reflection acentric: 13187 / Reflection centric: 2077

Phasing MAD set

Lowest resolution: 90 Å

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	0.97	0.93	3	12.2	16	0.4	0.34	12282	1645
2	0.94	0.91	2.5	46.2	61.2	0.68	0.5	13098	1906
3	1.95	1	3	0	0	0	0	12454	1999

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.66-19.98	0.95	0.85	14.5	15.6	0.75	0.64	193	78
1	7.27-10.66	0.85	0.72	8.9	11.8	1.04	0.84	543	141
1	5.52-7.27	0.89	0.8	8.7	11.1	0.9	0.72	1065	199
1	4.44-5.52	0.97	0.94	12.2	14.8	0.53	0.41	1770	273
1	3.72-4.44	0.98	0.97	13.4	20	0.37	0.24	2706	341
1	3.2-3.72	0.99	0.98	12.7	16.7	0.29	0.2	3774	402
1	2.81-3.2	0.99	1	12.4	17	0.23	0.15	2231	211
1	2.5-2.81	0	0	0	0	0	0	0	0
2	10.66-19.98	0.97	0.98	54.8	68.9	0.73	0.54	188	89
2	7.27-10.66	0.93	0.91	52.2	65.5	0.71	0.58	539	154
2	5.52-7.27	0.93	0.95	43.8	57.8	0.81	0.61	1089	232
2	4.44-5.52	0.95	0.9	56.5	69.7	0.6	0.47	1785	303
2	3.72-4.44	0.95	0.92	55.6	73.8	0.56	0.41	2715	372
2	3.2-3.72	0.94	0.9	44.8	53.9	0.66	0.51	3805	449
2	2.81-3.2	0.93	0.89	32.4	46.4	0.87	0.54	2977	307
2	2.5-2.81	0	0	0	0	0	0	0	0
3	10.66-19.98	1.22	1	0	0	0	0	197	107
3	7.27-10.66	1.43	1	0	0	0	0	554	182
3	5.52-7.27	2.55	1	0	0	0	0	1089	249
3	4.44-5.52	1.48	1	0	0	0	0	1812	333
3	3.72-4.44	1.44	1	0	0	0	0	2746	406
3	3.2-3.72	3.63	1	0	0	0	0	3810	479
3	2.81-3.2	11.74	1	0	0	0	0	2246	243
3	2.5-2.81	0	0	0	0	0	0	0	0

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	51.03	0.193	0.786	0.235	1.067	0.092
2	49.067	0.174	0.632	0.162	1.074	0.089
3	31.151	0.43	0.554	0.285	0.811	0.079
4	46.915	-0.088	0.849	0.127	0.866	0.074
5	49.436	-0.24	0.799	0.233	0.656	0.066
6	71.908	-0.477	0.723	0.173	0.532	0.055
7	134.072	-0.246	0.941	0.159	0.685	0.044
8	82.314	0.632	0.94	0.114	0.668	0.034
9	171.755	0.123	0.107	0.419	0.256	0.021
10	35.831	0.503	0.526	0.466	0.185	0.015
11	0.023	0.195	0.791	0.235	0.738	0.279
12	10.786	0.173	0.636	0.163	0.916	0.216
13	-3.902	0.432	0.556	0.286	0.589	0.303
14	15.731	-0.088	0.853	0.126	0.772	0.274
15	1.573	-0.239	0.803	0.234	0.47	0.261
16	20.578	-0.478	0.724	0.172	0.39	0.203
17	31.737	-0.245	0.939	0.159	0.408	0.193
18	35.407	0.629	0.942	0.114	0.649	0.145
19	37.875	0.117	0.094	0.441	0.271	0.087
20	63.639	0.503	0.525	0.47	0.313	0.122
21	57.958	0.192	0.785	0.235	1.128	0
22	50.665	0.174	0.631	0.162	1.336	0
23	56.458	0.428	0.553	0.285	0.986	0
24	53.786	-0.085	0.849	0.126	0.975	0
25	94.024	-0.245	0.801	0.235	1.035	0
26	82.519	-0.478	0.722	0.173	0.556	0
27	75.805	-0.25	0.942	0.154	0.438	0
28	111.981	0.628	0.942	0.118	0.72	0
29	83.244	0.129	0.105	0.433	0.257	0
30	101.857	0.503	0.528	0.469	0.247	0

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.66-19.98	0.434	0.485	0.341	304	197	107
7.27-10.66	0.487	0.486	0.492	736	554	182
5.52-7.27	0.469	0.471	0.461	1338	1089	249
4.44-5.52	0.344	0.346	0.335	2145	1812	333
3.72-4.44	0.291	0.285	0.33	3152	2746	406
3.2-3.72	0.275	0.268	0.327	4289	3810	479
2.81-3.2	0.27	0.261	0.36	3300	2979	321
2.5-2.81	0	0	0		0	0

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 24545

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.89-100	63.8	0.713	508
7.18-8.89	61.7	0.838	507
6.33-7.18	63.4	0.797	504
5.73-6.33	63.5	0.775	545
5.28-5.73	65	0.805	574
4.92-5.28	67.7	0.814	632
4.62-4.92	68.4	0.815	647
4.38-4.62	69.5	0.823	689
4.16-4.38	73.2	0.804	742
3.98-4.16	70.4	0.816	762
3.82-3.98	70.1	0.809	803
3.68-3.82	71.3	0.809	844
3.55-3.68	73.4	0.761	870
3.43-3.55	72	0.614	908
3.33-3.43	71.5	0.673	924
3.23-3.33	75.9	0.699	958
3.14-3.23	76.4	0.704	987
3.06-3.14	77.1	0.7	1014
2.99-3.06	79.1	0.685	1020
2.92-2.99	84.7	0.651	1072
2.85-2.92	91.4	0.652	1072
2.79-2.85	87.5	0.694	1104
2.73-2.79	89.1	0.709	1116
2.68-2.73	90.7	0.685	1163
2.63-2.68	92.2	0.651	1161
2.58-2.63	90.5	0.586	1229
2.5-2.58	88.6	0.417	2190

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
BUSTER-TNT		refinement
PDB_EXTRACT	3.1	data extraction
BOS		data collection
DENZO		data reduction
BUSTER	2.8.0	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.49→28.801 Å / Cor.coef. F_o:F_c: 0.9408 / Cor.coef. F_o:F_c free: 0.9149 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2271	1291	5.08 %	RANDOM
R_work	0.1773	-	-	-
all	0.1798	-	-	-
obs	0.1798	25411	-	-

Displacement parameters

B_iso max: 151.31 Å² / B_iso mean: 43.8182 Å² / B_iso min: 9.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.0641 Å²	0 Å²	0 Å²
2-	-	-2.6295 Å²	0 Å²
3-	-	-	7.6935 Å²

Refine analyze

Luzzati coordinate error obs: 0.295 Å

Refinement step

Cycle: LAST / Resolution: 2.49→28.801 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5355	0	12	182	5549

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	1888	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	121	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	811	HARMONIC	5
X-RAY DIFFRACTION	t_it	5502	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	675	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	6159	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	5502	HARMONIC	2	0.01
X-RAY DIFFRACTION	t_angle_deg	7488	HARMONIC	2	1.18
X-RAY DIFFRACTION	t_omega_torsion				3.04
X-RAY DIFFRACTION	t_other_torsion				21.05

LS refinement shell

Resolution: 2.49→2.59 Å / Total num. of bins used: 13

	R_factor	Num. reflection	% reflection
R_free	0.3016	125	4.87 %
R_work	0.2151	2441	-
all	0.2188	2566	-

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	2.0268	0.1459	0.7019	0.9537	-0.2297	2.4458	0.0123	0.0806	-0.1296	-0.0366	0.0281	-0.0446	0.1563	0.1821	-0.0404	-0.0508	-0.0039	0.013	-0.0905	0.0046	-0.0813	4.2489	9.4873	64.5555
2	4.836	0.3084	1.5778	3.1596	-0.2013	4.7453	-0.0103	0.3774	0.3865	-0.0894	-0.0805	0.2605	-0.4876	-0.008	0.0909	-0.072	0.0481	-0.0337	-0.2175	0.041	-0.1031	-32.4826	28.0711	16.533
3	1.9008	0.2695	0.4053	0.5089	0.0235	1.6733	-0.0552	0.3084	-0.0488	-0.0761	0.078	-0.0284	-0.0697	0.196	-0.0228	-0.085	-0.0558	-0.0089	-0.0142	-0.0059	-0.066	6.2892	22.192	42.1267
4	0.7935	0.1402	0.8008	0.6234	0.6547	1.9079	-0.0215	0.101	-0.1152	-0.0232	0.0258	0.0197	0.0075	0.2137	-0.0043	-0.058	-0.0076	-0.0096	-0.0574	-0.0287	-0.0126	-20.2404	7.1139	25.4335

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|12 - A\|163 }	A	12 - 163
2	X-RAY DIFFRACTION	2	{ B\|12 - B\|163 }	B	12 - 163
3	X-RAY DIFFRACTION	3	{ A\|164 - A\|361 }	A	164 - 361
4	X-RAY DIFFRACTION	4	{ B\|164 - B\|361 }	B	164 - 361

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