PDB-7mkv: Engineered PLP-dependent decarboxylative aldolase from Aspergillu...

ID or keywords:

Entry

Database: PDB / ID: 7mkv

Title

Engineered PLP-dependent decarboxylative aldolase from Aspergillus flavus, UstD2.0, bound as the internal aldimine

Components

Cysteine desulfurase-like protein ustD

Keywords

LYASE / TRANSFERASE / internal aldimine / PLP / enamine / directed evolution

Function / homology

Transferases / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / transferase activity / Cysteine desulfurase-like protein ustD

Function and homology information

Biological species

Aspergillus flavus (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.25 Å

Authors

Ellis, J.M. / Buller, A.R. / Bingman, C.A.

Funding support

United States, 1items

Citation

Journal: Nat Catal / Year: 2022
Title: Biocatalytic synthesis of non-standard amino acids by a decarboxylative aldol reaction
Authors: Ellis, J.M. / Campbell, M.E. / Kumar, P. / Geunes, E.P. / Bingman, C.A. / Buller, A.R.

History

Deposition	Apr 27, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mkv.cif.gz	476.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7mkv.ent.gz	406.9 KB	Display	PDB format
PDBx/mmJSON format	7mkv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mkv_validation.pdf.gz	453.2 KB	Display	wwPDB validaton report
Full document	7mkv_full_validation.pdf.gz	459.3 KB	Display
Data in XML	7mkv_validation.xml.gz	44 KB	Display
Data in CIF	7mkv_validation.cif.gz	61.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mk/7mkv ftp://data.pdbj.org/pub/pdb/validation_reports/mk/7mkv	HTTPS FTP

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Related structure data

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: Cysteine desulfurase-like protein ustD

B: Cysteine desulfurase-like protein ustD

C: Cysteine desulfurase-like protein ustD

149 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cysteine desulfurase-like protein ustD

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

2

B: Cysteine desulfurase-like protein ustD

C: Cysteine desulfurase-like protein ustD

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

Unit cell

Length a, b, c (Å)	162.090, 162.090, 221.005
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-550- HOH

#1: Protein	Cysteine desulfurase-like protein ustD / Ustiloxin B biosynthesis protein D Mass: 49595.137 Da / Num. of mol.: 3 / Mutation: I391T C392L L393M C122A C227A C236S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus (mold) / Gene: ustD, AFLA_095040 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8NM72, Transferases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.94 % / Description: Tetragonal prisms
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES, 6% Tacsimate, 16% PEG-MME 5K, 4.5% Ethylene Glycol Temp details: Room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.004 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 16, 2021
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.004 Å / Relative weight: 1
Reflection	Resolution: 2.25→40 Å / Num. obs: 133166 / % possible obs: 99.6 % / Redundancy: 14.2 % / CC_1/2: 0.999 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.25→2.31 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 9727 / CC_1/2: 0.443 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
Aimless		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.25→39.81 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.922 / SU B: 14.71 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	3418	5 %	RANDOM
R_work	0.2136	-	-	-
obs	0.2152	65625	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 105.29 Å² / B_iso mean: 42.72 Å² / B_iso min: 21.73 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.56 Å²	0 Å²	-0 Å²
2-	-	-0.56 Å²	0 Å²
3-	-	-	1.11 Å²

Refinement step

Cycle: final / Resolution: 2.25→39.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9449	0	0	275	9724
B_iso mean	-	-	-	38.57	-
Num. residues	-	-	-	-	1220

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	9746
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9148
X-RAY DIFFRACTION	r_angle_refined_deg	1.212	1.64	13323
X-RAY DIFFRACTION	r_angle_other_deg	1.096	1.568	21081
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.197	5	1233
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.452	21.39	439
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.514	15	1538
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.841	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	1321
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10906
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2171

LS refinement shell

Resolution: 2.254→2.312 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	220	-
R_work	0.313	4651	-
all	-	4871	-
obs	-	-	96.61 %

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	4.7291	0.4981	0.5059	0.8962	-1.2449	4.6524	-0.2826	0.1907	-0.2887	-0.2072	-0.1772	-0.4385	0.3831	1.0476	0.4598	0.0617	0.076	0.0951	0.8129	-0.0003	0.2259	56.529	-6.314	88.251
2	1.4893	0.1748	1.7727	2.4269	2.8577	5.8096	-0.1026	0.0015	0.1788	0.0372	0.0022	-0.0947	-0.1717	0.4955	0.1004	0.0649	-0.0135	0.0424	0.5172	0.0393	0.142	49.897	-0.303	103.963
3	1.6888	0.6212	3.7194	1.0949	2.7978	11.0009	-0.0748	-0.3723	-0.0527	0.0709	0.0037	0.0664	-0.4366	-0.3547	0.0711	0.4414	-0.1966	0.0135	0.5071	0.0474	0.2811	45.849	17.49	113.143
4	1.4738	0.0681	-0.2982	0.4905	0.5359	0.8968	0.0217	-0.0323	0.1385	0.0562	-0.0434	0.0607	0.0471	0.2396	0.0217	0.1908	-0.0298	-0.0221	0.367	0.0104	0.1008	24.035	3.223	99.767
5	1.2112	-0.4533	-0.0838	0.7804	0.0004	1.0913	0.0506	0.1178	-0.0556	-0.0113	-0.0637	0.0143	0.034	0.2436	0.0131	0.1855	-0.004	-0.0054	0.3072	-0.02	0.1198	22.247	-0.116	86.749
6	1.0757	-0.386	0.3806	0.5876	0.0317	1.0679	-0.0728	0.1199	-0.0671	-0.014	-0.0024	0.0051	-0.2218	0.3411	0.0752	0.1903	-0.1067	0.0121	0.3703	-0.0212	0.1083	29.697	8.099	99.892
7	2.4768	-0.232	-1.3249	1.1418	-0.1084	0.8123	-0.0109	-0.0488	0.0397	0.1538	-0.0239	-0.0982	-0.065	0.1762	0.0348	0.1375	-0.1198	-0.048	0.4831	0.0037	0.0826	40.398	8.769	102.258
8	1.4074	1.0287	-0.163	3.5772	-0.4581	1.8862	0.0218	0.1226	-0.1053	-0.2271	0.0023	-0.0899	0.2074	0.4423	-0.0242	0.1506	0.1369	0.025	0.4203	-0.0142	0.0948	40.205	-12.174	78.936
9	8.4527	0.1858	0.2214	1.1814	-2.0442	3.6903	-0.1582	-0.1044	-0.4859	-0.2198	-0.0039	-0.1004	0.4702	0.2337	0.1621	0.2615	0.2627	-0.0152	0.4691	-0.0126	0.0924	40.932	-22.226	92.23
10	2.7592	-0.0801	-0.6894	1.2966	-0.0498	1.3781	0.0597	0.1799	-0.3872	0.0044	-0.0897	-0.0409	0.3272	0.4064	0.03	0.2276	0.2013	-0.0083	0.4283	-0.0006	0.0699	40.276	-17.683	85.941
11	1.5059	0.2851	-0.2718	0.9589	0.5713	2.852	-0.0214	-0.1781	0.0723	0.0201	0.1039	-0.1529	0.1095	0.8315	-0.0824	0.0746	0.0212	-0.0023	0.5006	0.0212	0.13	53.15	-0.619	49.507
12	0.8203	-0.8568	-1.4315	3.6231	3.1872	10.9827	-0.0408	0.3106	-0.1225	-0.2504	0.0057	-0.1388	0.5993	-0.1585	0.0351	0.3005	0.1047	-0.0114	0.4209	-0.0042	0.3249	44.816	-20.586	33.173
13	1.4773	-0.2229	0.0795	0.3747	0.4173	0.7891	0.002	0.1285	-0.0966	-0.0403	-0.0084	0.0449	-0.015	0.2333	0.0064	0.2083	0.0202	0.0068	0.253	-0.0046	0.1314	24.137	-4.858	46.568
14	4.0677	2.5332	2.2043	3.0272	2.1333	1.6852	-0.0049	-0.0802	-0.0035	0.0846	-0.0029	0.0298	-0.0703	0.1402	0.0077	0.2794	-0.0915	0.015	0.3574	-0.02	0.1892	18.005	4.076	60.453
15	0.4789	0.0268	-0.2459	0.2134	-0.02	1.1345	0.0325	-0.0157	0.0156	-0.0122	-0.0129	-0.0124	0.1413	0.2594	-0.0196	0.1785	0.0475	-0.0124	0.2813	-0.0116	0.1385	27.149	-7.514	52.15
16	0.4218	0.2129	0.2037	0.72	0.1526	1.3953	0.0129	0.058	-0.0235	0.0027	0.0042	-0.1163	0.1075	0.4265	-0.0171	0.108	0.0464	-0.0065	0.3857	0.0033	0.1191	42.508	-5.053	52.695
17	1.6531	-0.3512	-0.7631	3.9577	-0.2607	2.1695	-0.0559	-0.0306	0.3135	0.0858	0.0636	-0.0344	-0.3214	0.4144	-0.0077	0.1781	-0.1309	-0.0628	0.3595	-0.0066	0.167	37.876	14.505	65.089
18	6.1724	1.0324	-0.2735	0.5301	-1.0436	2.824	0.1092	0.4614	0.2764	0.0573	-0.0216	0.063	-0.1858	0.2865	-0.0876	0.2572	-0.1664	0.0303	0.2354	-0.0182	0.2303	37.099	16.106	54.12
19	2.4748	-0.9088	0.3659	2.7409	0.6165	1.7982	0.0179	-0.1466	0.2779	-0.0219	0.0873	-0.0937	-0.249	0.3763	-0.1052	0.1743	-0.1622	-0.0039	0.3502	0.0142	0.0655	44.565	12.918	60.105
20	23.8079	-9.105	-0.8044	23.1137	-15.0447	12.0332	-0.3252	-0.4254	2.2189	0.9894	0.9154	-0.1895	-0.6584	-0.5806	-0.5902	0.5051	-0.1478	-0.0703	0.4063	-0.0292	0.2763	47.55	25.517	64.329
21	3.4216	-0.0569	1.7059	5.1592	2.3236	8.0865	-0.3131	0.3397	0.0187	-0.2963	0.3936	-0.4011	-0.2796	0.6518	-0.0805	0.0531	-0.0058	0.0336	0.5136	-0.0348	0.1381	55.818	-8.216	12.427
22	1.0259	0.3697	1.1467	2.6317	2.5674	3.3955	-0.0112	0.1805	0.1226	0.0602	0.0993	-0.2908	0.1061	0.5682	-0.0881	0.093	0.0419	0.0186	0.5008	0.0656	0.1743	50.23	-6.193	26.88
23	2.8854	-4.0198	-1.9136	5.935	1.0232	9.3343	-0.629	-0.2751	0.1179	1.1238	0.4269	-0.2228	-0.7903	-0.0881	0.2021	0.4018	-0.0948	-0.0819	0.4845	0.0197	0.0602	47.492	13.997	38.832
24	1.5414	0.3387	-0.1946	0.5553	0.1061	0.5031	0.061	0.0087	0.0958	0.104	-0.0304	-0.019	0.0124	0.1668	-0.0306	0.2027	-0.0175	0.0008	0.2718	0.0126	0.1281	24.753	1.596	24.954
25	1.6352	-0.5541	-0.4706	1.4659	0.3299	0.8635	0.0681	0.1146	-0.0273	-0.1169	-0.05	-0.0051	0.0616	0.1292	-0.018	0.1733	-0.0049	-0.005	0.275	-0.0144	0.1313	19.86	-2.157	12.091
26	0.2211	0.2099	0.3805	0.5952	0.017	1.0074	-0.0399	0.0955	0.0085	0.0392	-0.0366	0.0236	-0.1022	0.2278	0.0765	0.1616	-0.0472	0.0068	0.3404	0.0018	0.151	31.429	5.047	23.371
27	2.3185	-0.5107	-0.6012	1.1465	0.2603	0.582	-0.03	-0.121	0.2157	0.1068	0.0657	-0.1575	-0.1502	0.2191	-0.0357	0.1494	-0.0478	-0.0139	0.3333	-0.0254	0.1793	40.736	6.141	28.541
28	1.4758	0.0683	0.5722	2.2086	-0.0641	1.8212	0.0841	0.1788	-0.2249	-0.0837	-0.0292	-0.0242	0.19	0.3985	-0.0548	0.1313	0.1075	0.0297	0.3498	-0.0503	0.1542	39.445	-15.871	5.726
29	12.2615	-1.3977	1.7137	0.7428	-1.2741	2.2427	0.0296	-0.3429	-0.6725	-0.1267	-0.0719	0.0178	0.2551	0.1912	0.0423	0.2489	0.1447	-0.0276	0.3061	-0.0202	0.2717	40.679	-22.917	18.585
30	3.0276	0.1204	0.3202	0.8707	0.4813	0.845	0.0201	0.1749	-0.331	-0.1104	0.042	-0.0821	0.2809	0.1851	-0.0621	0.2384	0.151	0.0217	0.2889	-0.0095	0.1446	39.258	-20.502	11.263

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 53
2	X-RAY DIFFRACTION	2	A	54 - 79
3	X-RAY DIFFRACTION	3	A	80 - 100
4	X-RAY DIFFRACTION	4	A	101 - 159
5	X-RAY DIFFRACTION	5	A	160 - 243
6	X-RAY DIFFRACTION	6	A	244 - 285
7	X-RAY DIFFRACTION	7	A	286 - 322
8	X-RAY DIFFRACTION	8	A	323 - 369
9	X-RAY DIFFRACTION	9	A	370 - 395
10	X-RAY DIFFRACTION	10	A	396 - 437
11	X-RAY DIFFRACTION	11	B	31 - 79
12	X-RAY DIFFRACTION	12	B	80 - 100
13	X-RAY DIFFRACTION	13	B	101 - 157
14	X-RAY DIFFRACTION	14	B	158 - 192
15	X-RAY DIFFRACTION	15	B	193 - 286
16	X-RAY DIFFRACTION	16	B	287 - 341
17	X-RAY DIFFRACTION	17	B	342 - 377
18	X-RAY DIFFRACTION	18	B	378 - 402
19	X-RAY DIFFRACTION	19	B	403 - 430
20	X-RAY DIFFRACTION	20	B	431 - 437
21	X-RAY DIFFRACTION	21	C	32 - 49
22	X-RAY DIFFRACTION	22	C	50 - 77
23	X-RAY DIFFRACTION	23	C	78 - 100
24	X-RAY DIFFRACTION	24	C	101 - 157
25	X-RAY DIFFRACTION	25	C	158 - 232
26	X-RAY DIFFRACTION	26	C	233 - 286
27	X-RAY DIFFRACTION	27	C	287 - 320
28	X-RAY DIFFRACTION	28	C	321 - 377
29	X-RAY DIFFRACTION	29	C	378 - 395
30	X-RAY DIFFRACTION	30	C	396 - 437

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi