PDB-7u7h: Cysteate acyl-ACP transferase from Alistipes finegoldii

ID or keywords:

Entry

Database: PDB / ID: 7u7h

Title

Cysteate acyl-ACP transferase from Alistipes finegoldii

Components

7-keto-8-aminopelargonate synthetase-like enzyme

Keywords

TRANSFERASE / sulfonolipid biosynthesis / acyltransferase / Aminotransferase class I and II / Aminotran_1_2 / PLP-dependent alpha-oxoamine synthase

Function / homology

Function and homology information

biosynthetic process / pyridoxal phosphate binding / transferase activity
Similarity search - Function

Biological species

Alistipes finegoldii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Radka, C.D. / Miller, D.J. / Frank, M.W. / Rock, C.O.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	1K99AI166116-01	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	5R01GM034496-38	United States

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii.
Authors: Radka, C.D. / Miller, D.J. / Frank, M.W. / Rock, C.O.

History

Deposition	Mar 7, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7u7h.cif.gz	943.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7u7h.ent.gz	796.2 KB	Display	PDB format
PDBx/mmJSON format	7u7h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7u7h_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	7u7h_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7u7h_validation.xml.gz	86.8 KB	Display
Data in CIF	7u7h_validation.cif.gz	116.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u7/7u7h ftp://data.pdbj.org/pub/pdb/validation_reports/u7/7u7h	HTTPS FTP

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Related structure data

Related structure data	3a2bS S: Starting model for refinement
Similar structure data	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: 7-keto-8-aminopelargonate synthetase-like enzyme

B: 7-keto-8-aminopelargonate synthetase-like enzyme

C: 7-keto-8-aminopelargonate synthetase-like enzyme

D: 7-keto-8-aminopelargonate synthetase-like enzyme

E: 7-keto-8-aminopelargonate synthetase-like enzyme

F: 7-keto-8-aminopelargonate synthetase-like enzyme

hetero molecules

301 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 7-keto-8-aminopelargonate synthetase-like enzyme

B: 7-keto-8-aminopelargonate synthetase-like enzyme

hetero molecules

defined by author&software
Evidence: gel filtration
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 7-keto-8-aminopelargonate synthetase-like enzyme

F: 7-keto-8-aminopelargonate synthetase-like enzyme

defined by author&software
100 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: 7-keto-8-aminopelargonate synthetase-like enzyme

E: 7-keto-8-aminopelargonate synthetase-like enzyme

defined by author&software
100 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	127.516, 127.516, 177.300
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	7-keto-8-aminopelargonate synthetase-like enzyme Mass: 50036.500 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alistipes finegoldii (strain DSM 17242 / JCM 16770 / CCUG 46020 / CIP 107999 / KCTC 15236 / AHN 2437) (bacteria) Strain: DSM 17242 / JCM 16770 / CCUG 46020 / CIP 107999 / KCTC 15236 / AHN 2437 Gene: Alfi_1224 / Production host: Escherichia coli (E. coli) / References: UniProt: I3YKQ4
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.39 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 12% PEG 8000, 100 mM sodium cacodylate, 100 mM calcium acetate PH range: 5.0 - 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2020
Radiation	Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 2.9→29.55 Å / Num. obs: 71215 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC_1/2: 0.998 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.9→3.07 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 22569 / CC_1/2: 0.782 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1_4122	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XDS		data scaling
PHENIX	1.19.1_4122	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3A2B

3a2b

Resolution: 2.9→29.55 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2682	3557	5 %
R_work	0.2181	67521	-
obs	0.2206	71215	99.65 %

Solvent computation

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

Displacement parameters

B_iso max: 285.12 Å² / B_iso mean: 100.0168 Å² / B_iso min: 30 Å²

Refinement step

Cycle: final / Resolution: 2.9→29.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18469	0	30	0	18499
B_iso mean	-	-	61.86	-	-
Num. residues	-	-	-	-	2492

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.9-2.94	0.3746	133	0.3531	2538	2671	96
2.94-2.98	0.3535	146	0.3189	2778	2924	100
2.98-3.03	0.3541	142	0.3015	2691	2833	100
3.03-3.07	0.3313	144	0.2971	2718	2862	100
3.07-3.12	0.3544	142	0.3072	2688	2830	99
3.12-3.18	0.3346	143	0.2902	2708	2851	100
3.18-3.24	0.3322	139	0.26	2672	2811	100
3.24-3.3	0.2994	144	0.2595	2723	2867	100
3.3-3.37	0.288	142	0.2592	2683	2825	100
3.37-3.44	0.2806	142	0.249	2691	2833	100
3.44-3.52	0.3506	145	0.2461	2744	2889	99
3.52-3.61	0.2827	141	0.2413	2663	2804	100
3.61-3.7	0.3163	143	0.2414	2750	2893	100
3.7-3.81	0.2666	142	0.2275	2683	2825	100
3.81-3.93	0.2534	143	0.2074	2707	2850	100
3.94-4.08	0.2625	142	0.1952	2705	2847	100
4.08-4.24	0.2318	144	0.1909	2736	2880	100
4.24-4.43	0.2351	143	0.1877	2709	2852	100
4.43-4.66	0.2238	141	0.1789	2679	2820	100
4.66-4.95	0.2357	144	0.1765	2726	2870	100
4.95-5.33	0.2472	142	0.2014	2710	2852	100
5.34-5.87	0.2897	143	0.2281	2706	2849	100
5.87-6.71	0.2704	144	0.2307	2724	2868	100
6.71-8.42	0.2388	142	0.2163	2702	2844	100
8.42-29.55	0.2408	141	0.1777	2687	2828	99

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	0.2891	0.1399	0.5109	0.3998	0.0092	1.0754	-0.375	-0.5947	0.2173	0.329	0.366	0.1713	-0.5191	-0.7916	-0.0249	0.8465	0.4474	0.1235	0.63	0.0821	0.6081	-8.7041	52.8048	-19.9524
2	1.6857	0.3381	0.0951	1.1258	-0.0733	3.3612	-0.2184	0.0142	-0.0888	0.1618	0.2306	0.2148	0.5283	0.0021	-0.0284	0.5361	0.0063	0.0443	0.236	0.056	0.5806	0.3415	28.9736	-31.174
3	0.4139	0.0798	0.0936	1.3971	0.2438	2.4134	-0.2002	-0.0142	-0.1063	0.2494	0.2421	0.3493	1.1512	-0.4243	-0.0573	0.787	-0.1658	0.0988	0.3027	0.1161	0.6358	-6.1845	20.702	-31.2605
4	0.8437	0.0216	0.4378	1.5394	1.2452	1.9554	0.1231	-0.6011	-0.0176	0.6225	-0.2192	-0.0778	0.3786	-0.2808	0.0496	1.0062	0.1996	0.1036	0.4877	0.0989	0.5787	0.6496	31.2896	-6.9423
5	1.0426	0.2051	0.0347	0.5059	0.1145	1.0157	0.1549	-0.5958	0.1574	0.5665	0.2035	-0.0538	-0.3941	0.3225	-0.2311	1.1665	0.2544	0.0899	0.5361	0.0478	0.536	3.4503	39.782	-4.2906
6	0.3366	0.2304	-0.5918	0.2702	-0.256	1.2795	-0.3517	0.7313	-0.3747	0.0696	0.1941	0.3497	0.3503	-0.7068	0.0463	0.991	-0.441	-0.1993	1.0881	0.1792	0.9166	-13.8255	18.1255	-49.434
7	1.1926	0.2203	0.2966	1.2146	0.1597	3.199	-0.2289	-0.0475	0.0768	-0.2495	0.2565	0.1591	-0.4026	0.2298	-0.0004	0.4488	-0.0505	-0.0421	0.2122	0.0607	0.5056	3.1568	42.5188	-40.7824
8	1.9281	0.6522	-0.6733	0.8298	-0.0191	0.2966	-0.3461	0.3177	-0.1973	-0.3843	0.2981	0.7402	-0.4173	-1.3591	0.0497	0.7243	0.308	-0.1681	0.914	0.296	1.0536	-19.0782	52.2302	-46.4123
9	0.8041	-0.1145	0.2612	1.5271	0.1832	1.8155	-0.3042	0.4831	0.1417	-0.5887	0.3705	0.0502	-1.3505	-0.0478	-0.0472	0.8664	-0.0078	-0.161	0.0103	0.2207	0.5321	-0.2659	50.2069	-47.2542
10	0.4061	-0.0916	-0.059	1.6099	0.3672	1.5353	0.0483	0.5347	-0.1795	-0.6675	0.0759	0.1132	0.2055	0.126	-0.0838	1.0253	-0.264	-0.1132	0.5669	0.0315	0.6367	1.7469	33.9636	-66.0747
11	1.1435	0.6056	-0.4041	0.3537	-0.4235	1.6005	-0.0522	-0.4416	-0.0594	-0.1268	-0.2209	0.0062	0.6745	1.1915	0.0962	1.2007	0.0226	0.0351	0.8466	0.0516	0.7355	36.716	63.702	-77.302
12	1.6168	0.1743	-0.3714	2.0803	-0.5792	3.6797	-0.2258	0.2741	-0.1007	-0.2857	0.1426	-0.0634	0.9072	-0.5206	0.0848	1.0028	-0.396	0.0839	0.6145	0.0723	0.5914	20.914	65.5593	-95.3545
13	1.2286	0.0512	0.3538	0.5285	-0.8279	1.4263	-0.0277	0.0029	0.0036	-0.1357	0.0462	-0.0262	0.646	-0.278	-0.0655	1.1779	-0.2324	0.14	0.5183	0.0231	0.6143	23.21	62.2445	-76.1848
14	1.5547	-0.0978	0.2797	0.2793	0.4101	1.8531	-0.0627	-0.3316	0.3201	-0.285	0.1947	-0.1218	0.0546	0.3792	-0.1234	1.038	-0.3804	0.1123	0.8019	0.0129	0.6657	24.0461	71.9907	-62.5841
15	0.26	0.4675	-0.1315	0.7561	-0.2221	0.0618	-0.0549	0.2079	-0.3048	-0.0778	0.4611	-0.427	-0.4939	-0.2845	-0.0178	1.599	0.1736	-0.1019	1.2369	-0.0281	0.9627	-19.9507	36.5264	-112.7436
16	1.1774	0.1486	0.5209	1.2334	0.5401	4.122	0.1083	-0.0711	-0.0155	0.4085	-0.176	0.1691	0.9285	-0.8152	0.0305	0.9594	-0.3965	0.0038	0.6513	-0.0843	0.5682	-21.3338	13.7783	-98.3077
17	1.4895	-0.5965	-0.7039	1.4538	-0.6096	1.6065	0.2407	0.0026	0.2767	-0.4495	-0.1545	-0.3118	-0.065	0.115	-0.1213	1.0153	-0.3431	0.0788	0.7265	-0.1471	0.6868	-12.4554	19.6079	-126.0893
18	1.0904	0.2983	0.0773	0.9179	0.0805	0.4002	0.1214	-0.9966	0.1004	0.901	-0.1041	0.4196	0.0709	-1.2323	-0.0197	1.1662	-0.3407	0.2668	1.5358	-0.2398	0.7807	-37.5693	20.8871	-82.119
19	0.7181	-0.943	0.6791	1.7489	-0.3101	1.3075	0.4316	0.5039	0.9002	-0.3157	-0.1706	-0.0945	-0.1387	0.2131	-0.1672	0.993	-0.173	-0.1315	1.6166	0.0349	1.3655	-36.6453	27.1573	-109.7518
20	2.3827	0.7039	-0.7358	2.5175	0.0727	3.1678	0.3553	-0.5445	0.4629	0.6406	-0.3897	0.6014	-0.8929	-1.0822	0.0176	1.2126	0.1039	0.138	1.2244	-0.2804	0.927	-33.0083	38.9345	-86.8499
21	1.7455	0.0657	-0.3102	0.5878	-0.471	0.4443	-0.2093	0.8919	0.5431	-1.0722	0.2076	-0.0888	-1.0383	0.6813	0.0696	1.3282	-0.292	-0.124	1.7327	0.3729	0.8596	64.3332	6.2872	-48.469
22	0.7947	-0.8948	0.3397	1.4725	0.3584	1.3673	-0.3265	-0.3396	0.4558	-0.0678	0.5771	1.069	-0.4796	-0.8356	-0.169	1.4604	-0.4028	-0.0883	1.4274	0.0919	1.2066	58.3071	8.5902	-20.6619
23	2.6384	0.334	-0.2577	2.0489	-0.1804	1.8779	0.0159	0.8385	0.7778	-0.0197	0.0236	0.528	-0.9063	-0.5044	-0.0355	1.0537	0.2994	-0.1468	1.2351	0.1947	0.9184	37.6018	7.0226	-38.1862
24	1.3179	0.0724	0.1263	0.952	-0.2685	1.1341	0.0365	0.7802	0.5715	-0.5812	0.0344	-0.2522	-1.1908	0.3739	-0.0079	2.005	-0.3111	-0.0193	1.3649	0.3771	1.0886	57.5152	16.5088	-49.8406

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 32 )	A	1 - 32
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 163 )	A	33 - 163
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 164 through 301 )	A	164 - 301
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 302 through 373 )	A	302 - 373
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 374 through 423 )	A	374 - 423
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 22 )	B	1 - 22
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 23 through 148 )	B	23 - 148
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 149 through 199 )	B	149 - 199
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 200 through 354 )	B	200 - 354
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 355 through 423 )	B	355 - 423
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 75 )	C	1 - 75
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 76 through 272 )	C	76 - 272
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 273 through 354 )	C	273 - 354
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 355 through 411 )	C	355 - 411
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 47 )	D	1 - 47
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 48 through 321 )	D	48 - 321
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 322 through 410 )	D	322 - 410
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 1 through 61 )	E	1 - 61
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 62 through 90 )	E	62 - 90
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 91 through 423 )	E	91 - 423
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 1 through 61 )	F	1 - 61
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 62 through 90 )	F	62 - 90
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 91 through 272 )	F	91 - 272
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 273 through 423 )	F	273 - 423

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