PDB-6s54: Transaminase from Pseudomonas fluorescens

ID or keywords:

Entry

Database: PDB / ID: 6s54

Title

Transaminase from Pseudomonas fluorescens

Components

Aspartate aminotransferase family protein

Keywords

TRANSFERASE / class-I omega-transaminase / PLP / transaminase / Pyridoxal phosphate

Function / homology

Function and homology information

putrescine-pyruvate transaminase / transaminase activity / pyridoxal phosphate binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.21 Å

Authors

Smith, P. / Roura Padrosa, D. / Lopez-Gallego, F. / Paradisi, F. / Dreveny, I.

Funding support

United Kingdom, 1items

Citation

Journal: Front Bioeng Biotechnol / Year: 2019
Title: Enhancing PLP-Binding Capacity of Class-III omega-Transaminase by Single Residue Substitution.
Authors: Roura Padrosa, D. / Alaux, R. / Smith, P. / Dreveny, I. / Lopez-Gallego, F. / Paradisi, F.

History

Deposition	Jun 30, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6s54.cif.gz	693.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6s54.ent.gz	579.6 KB	Display	PDB format
PDBx/mmJSON format	6s54.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6s54_validation.pdf.gz	515.1 KB	Display	wwPDB validaton report
Full document	6s54_full_validation.pdf.gz	543.4 KB	Display
Data in XML	6s54_validation.xml.gz	64.9 KB	Display
Data in CIF	6s54_validation.cif.gz	89 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/6s54 ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s54	HTTPS FTP

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Related structure data

Related structure data	5lhaS S: Starting model for refinement
Similar structure data	5lha-d 4e3r-d 4e3q-d 6gio-d 6wj8-d 5lh9-d 5g2p-d 5wya-d 5g2q-1 1m0n-1 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

Deposited unit

A: Aspartate aminotransferase family protein

B: Aspartate aminotransferase family protein

C: Aspartate aminotransferase family protein

D: Aspartate aminotransferase family protein

hetero molecules

212 kDa, 4 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)	92.022, 94.544, 242.218
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 12 or resid 14 through 43 or resid 45 through 459))
2	1	(chain B and (resid 12 or resid 14 through 43 or resid 45 through 459))
3	1	(chain C and (resid 13 through 43 or resid 45 through 459))
4	1	(chain D and (resid 12 or resid 14 through 43 or resid 45 through 459))

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	ALA	ALA	(chain A and (resid 12 or resid 14 through 43 or resid 45 through 459))	A	A	12	32
1	2	LEU	LEU	GLY	GLY	(chain A and (resid 12 or resid 14 through 43 or resid 45 through 459))	A	A	14 - 43	34 - 63
1	3	GLY	GLY	TRP	TRP	(chain A and (resid 12 or resid 14 through 43 or resid 45 through 459))	A	A	45 - 459	65 - 479
2	1	ALA	ALA	ALA	ALA	(chain B and (resid 12 or resid 14 through 43 or resid 45 through 459))	B	B	12	32
2	2	LEU	LEU	GLY	GLY	(chain B and (resid 12 or resid 14 through 43 or resid 45 through 459))	B	B	14 - 43	34 - 63
2	3	GLY	GLY	TRP	TRP	(chain B and (resid 12 or resid 14 through 43 or resid 45 through 459))	B	B	45 - 459	65 - 479
3	1	TRP	TRP	GLY	GLY	(chain C and (resid 13 through 43 or resid 45 through 459))	C	C	13 - 43	33 - 63
3	2	GLY	GLY	TRP	TRP	(chain C and (resid 13 through 43 or resid 45 through 459))	C	C	45 - 459	65 - 479
4	1	ALA	ALA	ALA	ALA	(chain D and (resid 12 or resid 14 through 43 or resid 45 through 459))	D	D	12	32
4	2	LEU	LEU	GLY	GLY	(chain D and (resid 12 or resid 14 through 43 or resid 45 through 459))	D	D	14 - 43	34 - 63
4	3	GLY	GLY	TRP	TRP	(chain D and (resid 12 or resid 14 through 43 or resid 45 through 459))	D	D	45 - 459	65 - 479

#1: Protein	Aspartate aminotransferase family protein / omega-transaminase Mass: 52596.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: CQZ98_27790 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S8XV37, UniProt: A0A5E7M111*PLUS
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.5 Å³/Da / Density % sol: 50.88 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate, pH 5.6, 12% w/v PEG 6000, 0.1 M lithium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 11, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.21→92.05 Å / Num. obs: 106548 / % possible obs: 100 % / Redundancy: 6.5 % / CC_1/2: 0.973 / R_merge(I) obs: 0.309 / R_pim(I) all: 0.131 / R_rim(I) all: 0.336 / Net I/σ(I): 3.9 / Num. measured all: 692500 / Scaling rejects: 477

Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs
2.21-2.27	6.5	1.7	50050	7759	0.589	0.723	1.849	1
9.88-92.05	5.9	0.133	8082	1371	0.934	0.058	0.146	10.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.3	data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LHA

5lha

Resolution: 2.21→88.073 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.5

	R_factor	Num. reflection	% reflection
R_free	0.2444	5321	5 %
R_work	0.2128	-	-
obs	0.2144	106341	99.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 172.65 Å² / B_iso mean: 64.5522 Å² / B_iso min: 15.25 Å²

Refinement step

Cycle: final / Resolution: 2.21→88.073 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13838	0	82	328	14248
B_iso mean	-	-	56.44	38.86	-
Num. residues	-	-	-	-	1799

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	8504	X-RAY DIFFRACTION	8.624	TORSIONAL
1	2	B	8504	X-RAY DIFFRACTION	8.624	TORSIONAL
1	3	C	8504	X-RAY DIFFRACTION	8.624	TORSIONAL
1	4	D	8504	X-RAY DIFFRACTION	8.624	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2096-2.2347	0.3515	179	0.3537	3191	3370	96
2.2347-2.261	0.3637	172	0.3534	3367	3539	100
2.261-2.2885	0.4041	157	0.3354	3297	3454	100
2.2885-2.3175	0.3732	180	0.3281	3351	3531	100
2.3175-2.348	0.3323	157	0.327	3339	3496	100
2.348-2.3802	0.4003	175	0.3128	3329	3504	100
2.3802-2.4142	0.3536	140	0.3105	3392	3532	100
2.4142-2.4502	0.3448	166	0.296	3334	3500	100
2.4502-2.4885	0.3384	194	0.2707	3360	3554	100
2.4885-2.5293	0.2984	187	0.2799	3268	3455	100
2.5293-2.5729	0.2906	182	0.2735	3343	3525	100
2.5729-2.6197	0.315	162	0.2491	3379	3541	100
2.6197-2.6701	0.2961	184	0.2379	3317	3501	100
2.6701-2.7246	0.2596	164	0.2288	3375	3539	100
2.7246-2.7839	0.2275	141	0.23	3388	3529	100
2.7839-2.8486	0.3112	165	0.2311	3346	3511	100
2.8486-2.9199	0.3209	171	0.2298	3367	3538	100
2.9199-2.9988	0.2631	183	0.2218	3344	3527	100
2.9988-3.0871	0.2842	170	0.2169	3375	3545	100
3.0871-3.1867	0.2676	162	0.2194	3372	3534	100
3.1867-3.3006	0.2336	197	0.2066	3360	3557	100
3.3006-3.4328	0.245	175	0.1988	3346	3521	100
3.4328-3.589	0.2288	193	0.19	3387	3580	100
3.589-3.7782	0.227	190	0.1877	3389	3579	100
3.7782-4.0149	0.2014	181	0.1723	3386	3567	100
4.0149-4.3249	0.1878	205	0.1627	3388	3593	100
4.3249-4.7601	0.1841	187	0.1535	3413	3600	100
4.7601-5.4489	0.1779	190	0.1656	3435	3625	100
5.4489-6.8646	0.2172	218	0.1821	3444	3662	100
6.8646-88.143	0.177	194	0.1723	3638	3832	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	0.0061	0.0006	-0.0068	-0.0016	-0.0137	-0.0096	0.0276	0.0327	-0.0335	-0.1379	0.0142	0.0984	0.0047	-0.0124	-0	0.1439	-0.0137	0.0262	0.2054	-0.0168	0.4055	55.3942	16.9673	180.8637
2	0.0079	0.0008	-0.0089	0.0189	0.0115	0	-0.0813	-0.0684	-0.1923	0.0061	-0.1049	0.1244	0.11	-0.0127	-0	0.2407	0.0058	0.0364	0.2336	0.0309	0.3725	65.1293	10.3792	183.424
3	0.0426	0.0051	-0.0287	0.0069	0.0053	0.077	-0.0305	-0.0609	0.08	-0.0018	0.0736	0.0323	0.0148	0.0407	0	0.1472	0.0054	0.001	0.169	-0.0241	0.173	78.0334	34.7805	189.2523
4	0.1175	-0.0293	0.0303	0.1267	0.0875	0.0451	-0.0145	0.0197	-0.0284	-0.0404	0.0384	-0.0332	-0.0094	0.009	0	0.148	-0.0062	0.0285	0.1596	-0.0408	0.1484	85.4587	29.6332	165.7312
5	-0.0084	-0.0129	-0.0058	0.0194	0.0013	0.0115	-0.069	-0.1053	0.0407	-0.0224	-0.0044	0.0217	0.006	0.0452	0	0.129	-0.0167	-0.0141	0.1266	-0.0416	0.194	81.0473	46.7349	175.6788
6	0.0138	0.0165	-0.0184	0.0092	-0.0342	0.0614	0.0239	-0.047	-0.2142	0.0228	0.0145	-0.1036	-0.0512	0.0024	0	0.2004	0.0313	-0.0187	0.2466	-0.0169	0.2265	86.8951	16.2765	185.0705
7	0.0302	0.0449	-0.0618	0.0768	-0.0206	0.0132	-0.038	-0.0389	-0.2101	-0.0192	0.0263	0.1604	-0.0254	0.0068	0	0.1702	0.0131	-0.0396	0.1813	-0.0282	0.2563	78.7704	4.392	173.5829
8	0.0022	0.0002	-0.0125	-0.0019	-0.0062	0.0018	-0.0108	-0.0185	0.0292	-0.0394	0.0457	0.0077	0.0114	0.0327	-0	0.1983	-0.0238	0.0094	0.212	-0.0655	0.3382	81.824	50.9473	187.887
9	0.0021	-0.0054	-0.0166	-0.0101	-0.0141	0.0306	-0.0159	-0.1888	-0.0118	0.1015	0.0255	0.0359	-0.0169	-0.0095	-0	0.2263	0.0126	0.0592	0.2559	-0.0439	0.2831	63.9786	41.8253	195.9273
10	0.0486	-0.034	-0.0995	0.0741	0.0863	0.0961	0.0128	-0.0013	0.0448	-0.0328	-0.0267	0.1864	0.0168	0.0194	0	0.1579	-0.0056	-0.0468	0.1598	0.0062	0.2923	59.7621	37.5845	168.9538
11	0.0643	-0.0352	-0.0687	0.0939	0.0585	0.0271	0.0741	0.0147	0.0807	-0.0022	0.0244	0.4577	0.0386	0.0439	0	0.1617	-0.0043	-0.0827	0.1704	0.0083	0.2889	50.8649	43.6368	168.5009
12	0.0757	-0.0043	-0.0509	-0.003	0.0847	-0.131	0.0403	-0.0154	0.0304	0.1466	0.0934	0.2715	0.3803	0.0663	0	0.0986	-0.0214	0.0552	0.1788	-0.0099	0.3021	54.0598	36.481	179.6347
13	0.0151	-0.0128	-0.0023	0.0148	0.0024	0.0136	0.0681	-0.0754	0.01	-0.0095	0.0406	0.108	0.0431	0.2483	0	0.1555	-0.0385	0.1089	0.1048	-0.0195	0.4586	60.2918	65.1385	181.1168
14	0.0085	-0.012	0.0085	0.0028	0.0145	0.0363	0.0888	-0.0022	0.0654	0.2161	0.0659	-0.0127	0.0521	0.0782	0	0.2127	0.0047	0.1027	0.2235	-0.0542	0.4071	58.4356	60.2438	190.2288
15	-0.0364	0.0569	0.0065	-0.0238	-0.0106	0.0361	0.2824	0.2449	-0.0251	-0.2372	-0.0933	0.0005	-0.0716	-0.1733	0	1.1748	0.0042	0.0654	0.8194	0.2203	0.0847	67.3622	48.9713	119.801
16	0.061	-0.0004	-0.0094	0.0696	-0.0246	0.0314	0.1248	-0.1223	0.2801	-0.2805	-0.0047	0.0578	0.0197	0.0545	-0	0.4154	0.0104	0.0157	0.2672	0.0941	0.3468	67.5486	56.4686	142.7826
17	0.003	0.0198	0.0265	-0.0052	-0.0162	0.0205	0.0537	0.0788	0.036	-0.4246	-0.0308	-0.0795	-0.1673	-0.1133	-0	0.8621	-0.0199	-0.4757	0.6763	0.4966	0.1952	47.8879	56.5061	125.0234
18	-0.0029	0.0039	-0.0016	0.0051	0.0048	0.0011	-0.0194	-0.0143	0.0059	0.0177	0.005	0.0086	0.0207	0.0026	0	1.1125	-0.1063	0.3805	0.88	0.1014	0.9324	91.6648	59.4393	129.6608
19	-0.0053	0.008	0.0003	-0.0146	-0.005	-0.0006	0.0147	0.0292	-0.022	-0.0308	-0.073	-0.0159	0.0091	-0.0379	-0	1.3074	0.1152	0.2191	1.0487	0.1731	0.6331	86.9092	45.4028	113.5051
20	0.0093	-0.0684	0.0369	-0.0135	0.0242	0.0652	0.3438	-0.0542	0.0191	-0.4838	0.0294	-0.0742	0.0627	-0.1827	0	0.7708	-0.0039	0.1683	0.3074	-0.4442	-0.7595	78.3442	29.1919	135.3298
21	-0.0073	0.0087	0.0286	-0.0065	-0.0157	0.0423	0.0738	0.0858	-0.02	-0.4162	0.0312	0.0642	0.0616	0.017	0	1.0463	0.0242	0.0368	0.9119	-0.0555	0.3344	78.0191	31.0816	123.7908
22	0.0065	0.0097	-0.0203	-0.0144	0.0137	0.003	-0.027	0.1294	0.1185	-0.1862	-0.2122	-0.1021	0.0371	0.017	-0	0.6349	-0.0326	1.3295	0.6517	-0.1865	-0.066	104.1207	37.9553	128.1687

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 7 through 28 )	A	7 - 28
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 60 )	A	29 - 60
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 124 )	A	61 - 124
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 302 )	A	125 - 302
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 303 through 334 )	A	303 - 334
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 335 through 374 )	A	335 - 374
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 375 through 459 )	A	375 - 459
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 10 through 39 )	B	10 - 39
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 85 )	B	40 - 85
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 201 )	B	86 - 201
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 202 through 302 )	B	202 - 302
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 303 through 374 )	B	303 - 374
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 375 through 419 )	B	375 - 419
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 420 through 459 )	B	420 - 459
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 13 through 124 )	C	13 - 124
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 125 through 334 )	C	125 - 334
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 335 through 459 )	C	335 - 459
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 11 through 39 )	D	11 - 39
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 40 through 85 )	D	40 - 85
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 86 through 302 )	D	86 - 302
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 303 through 374 )	D	303 - 374
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 375 through 459 )	D	375 - 459

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