PDB-7p3t: Transaminase of gamma-proteobacterium

ID or keywords:

Entry

Database: PDB / ID: 7p3t

Title

Transaminase of gamma-proteobacterium

Components

Branched-chain amino acid aminotransferase

Keywords

TRANSFERASE / transaminase / pyridoxal-phosphate

Function / homology

Function and homology information

branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity
Similarity search - Function

Biological species

Luminiphilus syltensis NOR5-1B (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Ermler, U.

Citation

Journal: Chem.Commun.(Camb.) / Year: 2021
Title: Rational engineering of Luminiphilus syltensis ( R )-selective amine transaminase for the acceptance of bulky substrates.
Authors: Konia, E. / Chatzicharalampous, K. / Drakonaki, A. / Muenke, C. / Ermler, U. / Tsiotis, G. / Pavlidis, I.V.

History

Deposition	Jul 8, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 15, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7p3t.cif.gz	732.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7p3t.ent.gz	610.3 KB	Display	PDB format
PDBx/mmJSON format	7p3t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7p3t_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	7p3t_full_validation.pdf.gz	2.1 MB	Display
Data in XML	7p3t_validation.xml.gz	75.7 KB	Display
Data in CIF	7p3t_validation.cif.gz	109.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p3/7p3t ftp://data.pdbj.org/pub/pdb/validation_reports/p3/7p3t	HTTPS FTP

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Related structure data

Related structure data	5cm0S S: Starting model for refinement
Similar structure data	1iyd-1 1iye-1 1i1m-1 1i1l-1 5cm0-1 4tny-d 2ej3-1 7lu5-2 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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (5)

Deposited unit

A: Branched-chain amino acid aminotransferase

B: Branched-chain amino acid aminotransferase

C: Branched-chain amino acid aminotransferase

D: Branched-chain amino acid aminotransferase

E: Branched-chain amino acid aminotransferase

F: Branched-chain amino acid aminotransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	86.810, 144.580, 151.760
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Branched-chain amino acid aminotransferase Mass: 33831.160 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Luminiphilus syltensis NOR5-1B (bacteria) Gene: ilvE_3, NOR51B_30 / Production host: Escherichia coli (E. coli) References: UniProt: B8KQT8, branched-chain-amino-acid transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1263 / Source method: isolated from a natural source / Formula: H₂O
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: 2.35 Å³/Da / Density % sol: 47.57 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 3350 0.2 M NaNO3

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 25, 2020

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.6→45.933 Å / Num. obs: 250022 / % possible obs: 99.7 % / Redundancy: 9.101 % / B_iso Wilson estimate: 33.559 Å² / CC_1/2: 1 / R_merge(I) obs: 0.036 / R_rim(I) all: 0.038 / Χ²: 0.938 / Net I/σ(I): 32.66 / Num. measured all: 2275575 / Scaling rejects: 59308

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.6-1.7	5.532	0.879	2.04	224276	41305	40538	0.719	0.968	98.1
1.7-1.9	9.715	0.308	7.8	572194	58909	58901	0.981	0.325	100
1.9-2.2	9.937	0.102	21.99	527072	53042	53042	0.998	0.108	100
2.2-2.7	10.111	0.048	43.72	448086	44318	44317	0.999	0.051	100
2.7-3.4	9.369	0.027	68.36	245777	26239	26233	1	0.029	100
3.4-4.2	9.933	0.021	96.85	124152	12503	12499	1	0.022	100
4.2-6	9.229	0.019	101.95	86546	9382	9378	1	0.02	100
6-8	9.309	0.018	104.95	27107	2915	2912	1	0.02	99.9
8-12	9.69	0.016	117.92	14806	1530	1528	1	0.016	99.9
12-45.933	8.248	0.016	108.13	5559	714	674	1	0.017	94.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5cm0

5cm0

Resolution: 1.6→45.933 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1847	12303	4.92 %
R_work	0.1687	237577	-
obs	0.1695	249880	99.67 %

Solvent computation

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

Displacement parameters

B_iso max: 106.1 Å² / B_iso mean: 32.8809 Å² / B_iso min: 18.03 Å²

Refinement step

Cycle: final / Resolution: 1.6→45.933 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13932	0	126	1273	15331
B_iso mean	-	-	31.02	35.88	-
Num. residues	-	-	-	-	1772

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.6-1.6182	0.3188	391	0.3194	7494	96
1.6182-1.6372	0.3442	399	0.303	7646	97
1.6372-1.6572	0.3177	395	0.2716	7801	99
1.6572-1.6782	0.2662	409	0.2497	7826	99
1.6782-1.7003	0.2622	403	0.2342	7883	100
1.7003-1.7235	0.2422	387	0.2224	7871	100
1.7235-1.7482	0.2576	418	0.2498	7872	100
1.7482-1.7743	0.2658	440	0.2364	7871	100
1.7743-1.802	0.2307	390	0.2194	7918	100
1.802-1.8315	0.2438	411	0.2057	7853	100
1.8315-1.8631	0.2257	408	0.1881	7897	100
1.8631-1.897	0.2033	384	0.1833	7954	100
1.897-1.9335	0.2213	420	0.187	7886	100
1.9335-1.9729	0.2076	374	0.1777	7957	100
1.9729-2.0158	0.2122	368	0.18	7938	100
2.0158-2.0627	0.2009	393	0.1788	7913	100
2.0627-2.1143	0.191	396	0.1761	7924	100
2.1143-2.1715	0.2137	402	0.169	7933	100
2.1715-2.2354	0.1778	447	0.1648	7875	100
2.2354-2.3075	0.1851	438	0.1619	7924	100
2.3075-2.39	0.1797	402	0.1591	7906	100
2.39-2.4857	0.1815	388	0.1647	8034	100
2.4857-2.5988	0.1869	398	0.1673	7942	100
2.5988-2.7358	0.2012	415	0.1633	7962	100
2.7358-2.9072	0.189	450	0.1721	7980	100
2.9072-3.1316	0.1773	394	0.1614	8007	100
3.1316-3.4467	0.1751	424	0.1636	8032	100
3.4467-3.9452	0.1656	402	0.1557	8073	100
3.9452-4.9696	0.1383	458	0.1282	8090	100
4.9696-45.932	0.1686	499	0.1725	8315	100

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	4.4343	1.924	1.5178	4.3971	-0.6264	2.9225	0.1484	-0.4531	-0.1392	0.401	-0.1594	0.1618	0.1735	-0.2136	-0.0771	0.2068	0.0056	0.0383	0.1701	0.0149	0.1995	22.6992	-33.5605	-7.3899
2	3.946	0.867	-1.7116	2.6317	-0.6533	3.3547	-0.0745	0.0342	-0.1144	-0.0827	0.0627	0.1223	0.1996	-0.09	0.0126	0.1635	-0.0206	-0.001	0.1395	0.0213	0.1654	17.8686	-31.6004	-20.1371
3	0.605	-0.3215	0.1741	2.3765	-0.2658	0.6122	-0.0077	0.0018	0.0081	-0.0343	0.0364	0.3094	0.0075	-0.1759	-0.036	0.1467	-0.0116	0.0133	0.2102	0.0331	0.1985	13.7858	-9.9836	-20.9712
4	1.6355	-0.9284	0.4162	7.0046	-0.6094	1.5492	0.0233	0.0951	-0.4253	-0.069	0.1183	1.5081	0.2256	-0.3446	-0.1372	0.2266	-0.0814	-0.0378	0.375	0.0738	0.568	-1.1991	-22.1248	-23.5039
5	4.1421	-0.0174	2.5699	4.7409	1.2313	3.0585	-0.1745	-0.359	0.3886	0.1651	0.0333	0.307	-0.5282	-0.3459	0.2089	0.3256	0.0426	0.0665	0.2144	0.0295	0.2879	21.0899	37.2079	-19.5976
6	2.3526	-0.2407	0.9176	3.0242	1.4991	5.0947	-0.0002	0.0246	0.2663	-0.055	0.0143	-0.0303	-0.5275	0.0506	0.0222	0.264	-0.0198	0.0499	0.157	0.0238	0.2516	34.4746	33.7343	-17.7794
7	0.6956	-0.1897	0.0607	1.9074	-0.3465	1.2597	0.0101	-0.065	0.1237	0.1948	0.0157	-0.1088	-0.2084	0.0423	-0.0372	0.1832	0.0037	0.0171	0.1709	-0.003	0.1834	35.2851	15.0006	-9.2594
8	5.7771	-0.8494	3.8153	5.8684	-3.636	7.6869	0.1812	-0.1224	-0.5898	0.0433	0.0494	0.0856	0.3807	0.0651	-0.2502	0.1704	0.0051	0.0332	0.1866	0.009	0.1921	31.9885	-30.0841	-1.1279
9	3.5952	-1.6245	1.2952	2.8096	-0.9065	1.7389	-0.0724	-0.1943	0.0709	0.2939	0.0661	-0.1313	-0.0519	0.0214	0.0298	0.1807	0.0003	-0.007	0.1945	0.0159	0.1658	42.9159	-19.0879	0.9337
10	5.0796	-2.6232	0.2363	6.1432	-0.2084	4.1259	-0.2749	-0.415	-0.3628	0.338	0.2672	1.0374	-0.3031	-0.7443	-0.0045	0.2319	0.027	0.0239	0.2632	0.0411	0.2826	26.1062	-19.1652	-0.4218
11	0.5166	0.1476	-0.1261	1.0652	-0.2565	1.8727	-0.0189	0.0138	-0.0792	-0.0021	-0.0105	-0.1324	0.1271	0.1233	0.0215	0.157	0.0068	0.0117	0.1859	0.0222	0.1998	46.5005	-17.3499	-21.4916
12	0.5026	0.1021	-0.4355	0.9096	-0.7091	2.795	0.0133	-0.0673	-0.0375	0.1168	-0.1311	-0.2609	-0.1111	0.5525	0.096	0.1763	-0.021	-0.0173	0.2717	0.0404	0.2732	57.5327	-13.0304	-15.986
13	2.9355	1.2896	0.6747	1.5974	1.1378	2.3697	-0.1461	0.3609	0.0968	-0.5219	0.2405	-0.3751	-0.3206	0.4597	-0.0632	0.3111	-0.0385	0.1489	0.3048	0.0009	0.3515	63.4139	-0.4911	-54.9363
14	2.3055	0.4486	-0.7415	2.8737	-0.2854	2.03	-0.0265	0.0471	-0.0955	-0.2593	0.1211	-0.6088	-0.0097	0.393	-0.0626	0.2104	-0.0047	0.1008	0.2808	-0.0083	0.3246	64.9051	-5.5761	-47.3182
15	0.8197	-0.5026	-0.4508	1.4513	0.7117	1.0706	0.0331	0.0249	0.1788	-0.181	0.0713	-0.295	-0.1704	0.2148	-0.1087	0.1987	-0.0402	0.0508	0.216	0.0094	0.239	51.8723	11.9891	-38.0926
16	1.7727	-1.0432	-0.9761	3.418	1.5572	2.9038	0.0127	-0.2018	0.3892	-0.2342	0.447	-1.1174	-0.1445	0.6649	-0.3323	0.2404	-0.1054	0.1072	0.4676	-0.1141	0.6797	70.915	15.5558	-37.4909
17	2.5157	0.5595	1.9915	2.2751	1.2984	3.2097	-0.1641	0.1235	0.416	-0.2728	0.0212	0.3492	-0.6484	-0.2199	0.1526	0.2992	0.0754	0.0415	0.2577	0.0813	0.308	9.4452	29.929	-29.8424
18	3.3424	-0.7356	0.6596	4.2565	-0.8217	3.3778	0.0094	-0.0368	0.1782	0.0179	0.0611	0.4118	-0.3762	-0.538	-0.0609	0.1977	0.0902	0.0328	0.2511	0.0361	0.2643	5.3931	22.5839	-27.4705
19	1.0872	-0.1558	-0.5534	0.8738	0.3635	1.4633	0.0574	0.1569	0.1736	-0.1458	0.0234	0.092	-0.2397	-0.1558	-0.0825	0.2124	0.0181	-0.0018	0.1909	0.0445	0.2061	21.8988	16.6114	-39.6533
20	4.309	-1.1994	-1.4771	1.7929	0.6428	2.7898	0.0671	0.4974	-0.0036	-0.2195	-0.109	0.2995	-0.0985	-0.5869	0.0415	0.2149	0.0092	-0.0485	0.2685	0.0145	0.2061	14.0114	10.7067	-49.836
21	3.7213	2.1187	0.3202	2.0373	0.7409	2.1313	-0.0985	0.3661	-0.2715	-0.4111	0.1472	-0.3171	0.0554	0.2059	-0.0636	0.3671	0.0352	0.0724	0.2309	0.0215	0.227	46.5716	-9.4095	-65.9133
22	2.3013	0.2707	-0.6784	4.5249	0.3092	3.4878	0.0085	0.2864	0.1565	-0.6682	0.0438	-0.106	-0.3241	-0.0231	-0.0316	0.3098	0.0137	0.0364	0.2376	0.0443	0.1642	39.3067	-3.5099	-65.7122
23	0.9125	0.1158	-0.3342	0.8018	-0.1995	1.4695	0.0225	0.0789	-0.0328	-0.1778	-0.0126	-0.0602	-0.0114	0.0496	-0.0028	0.2236	0.0047	0.0164	0.2158	0.003	0.212	35.716	-14.2633	-48.3682
24	0.9778	0.1582	0.1912	1.7918	-0.384	2.509	0.0071	0.1648	-0.0738	-0.3284	0.0241	0.1728	0.1038	-0.1511	-0.023	0.1744	-0.0007	-0.0147	0.1708	-0.0066	0.1733	25.9259	-23.2343	-50.2024

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 106 )	A	33 - 106
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 270 )	A	107 - 270
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 271 through 296 )	A	271 - 296
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 32 )	B	2 - 32
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 33 through 106 )	B	33 - 106
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 300 )	B	107 - 300
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 2 through 32 )	C	2 - 32
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 33 through 96 )	C	33 - 96
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 97 through 119 )	C	97 - 119
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 120 through 203 )	C	120 - 203
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 204 through 295 )	C	204 - 295
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 2 through 47 )	D	2 - 47
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 48 through 106 )	D	48 - 106
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 107 through 270 )	D	107 - 270
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 271 through 296 )	D	271 - 296
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 2 through 47 )	E	2 - 47
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 48 through 106 )	E	48 - 106
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 107 through 203 )	E	107 - 203
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 204 through 295 )	E	204 - 295
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 2 through 47 )	F	2 - 47
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 48 through 106 )	F	48 - 106
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 107 through 223 )	F	107 - 223
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 224 through 295 )	F	224 - 295

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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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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Data collection

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Phasing

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi