PDB-4a72: Crystal structure of the omega transaminase from Chromobacterium ...

ID or keywords:

Entry

Database: PDB / ID: 4a72

Title

Crystal structure of the omega transaminase from Chromobacterium violaceum in a mixture of apo and PLP-bound states

Components

OMEGA TRANSAMINASE

Keywords

TRANSFERASE / PLP-BINDING ENZYME / TRANSAMINASE FOLD TYPE I

Function / homology

Function and homology information

adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function

Biological species

CHROMOBACTERIUM VIOLACEUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Logan, D.T. / Hakansson, M. / Yengo, K. / Svedendahl Humble, M. / Engelmark Cassimjee, K. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P.

Citation

Journal: FEBS J. / Year: 2012
Title: Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp.
Authors: Svedendahl Humble, M. / Engelmark Cassimjee, K. / Hakansson, M. / Kimbung, Y.R. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. / Logan, D.T.

History

Deposition	Nov 10, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 1, 2012	Group: Database references
Revision 1.2	Jan 17, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	4a72.cif.gz	700.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4a72.ent.gz	582.3 KB	Display	PDB format
PDBx/mmJSON format	4a72.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4a72_validation.pdf.gz	475.2 KB	Display	wwPDB validaton report
Full document	4a72_full_validation.pdf.gz	488.5 KB	Display
Data in XML	4a72_validation.xml.gz	64.5 KB	Display
Data in CIF	4a72_validation.cif.gz	88.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a7/4a72 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a72	HTTPS FTP

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Related structure data

Related structure data	4a6rSC 4a6tC 4a6uC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ba4-d 4a6r-d 4ba5-d 4a6u-d 1c9c-1 1bqa-d 2x5f-d 4aja-1 3zrr-d 7aat-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: OMEGA TRANSAMINASE

B: OMEGA TRANSAMINASE

C: OMEGA TRANSAMINASE

D: OMEGA TRANSAMINASE

hetero molecules

206 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: OMEGA TRANSAMINASE

B: OMEGA TRANSAMINASE

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

2

C: OMEGA TRANSAMINASE

D: OMEGA TRANSAMINASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.350, 62.120, 119.240
Angle α, β, γ (deg.)	105.27, 90.66, 104.43
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.08323, -0.9675, -0.2387), (-0.9613, -0.1411, 0.2367), (-0.2626, 0.2098, -0.9418)	-37.88, -22.15, -78.44
2	given	(0.9776, -0.1988, 0.06912), (0.197, 0.9799, 0.03139), (-0.07397, -0.01706, 0.9971)	-0.2474, -10.84, 55.49
3	given	(0.2532, -0.894, -0.3695), (-0.9337, -0.3258, 0.1483), (-0.253, 0.3075, -0.9173)	-39.53, -43.38, -19.23

#1: Protein	OMEGA TRANSAMINASE Mass: 51279.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.06 Å³/Da / Density % sol: 40.4 % / Description: NONE
Crystal grow	pH: 7.4 Details: 200 NL OF PROTEIN AT 12 MG/ML IN 1 MM CYCLOSERINE MIXED WITH 200 NL OF RESERVOIR CONSISTING OF 0.1 M HEPES PH 7.5, 150-300 MM NACL AND 22.5-27.5% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 6, 2011 / Details: MULTILAYER MIRROR, VERTICALLY FOCUSING
Radiation	Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→30 Å / Num. obs: 61839 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / B_iso Wilson estimate: 27.53 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.4→2.45 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 82.6

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6R

4a6r

Resolution: 2.4→26.391 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 26.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2394	3139	5.1 %
R_work	0.1729	-	-
obs	0.1763	61746	96.39 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 33.401 Å² / k_sol: 0.365 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.487 Å²	4.6434 Å²	2.0306 Å²
2-	-	-1.734 Å²	-4.874 Å²
3-	-	-	-2.753 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→26.391 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13841	0	30	528	14399

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14235
X-RAY DIFFRACTION	f_angle_d	0.639	19265
X-RAY DIFFRACTION	f_dihedral_angle_d	12.732	5141
X-RAY DIFFRACTION	f_chiral_restr	0.038	2003
X-RAY DIFFRACTION	f_plane_restr	0.002	2514

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.4375	0.3335	147	0.2345	2541	X-RAY DIFFRACTION	92
2.4375-2.4774	0.3097	117	0.2381	2688	X-RAY DIFFRACTION	96
2.4774-2.5201	0.3817	132	0.2337	2624	X-RAY DIFFRACTION	96
2.5201-2.5659	0.3795	127	0.2364	2674	X-RAY DIFFRACTION	96
2.5659-2.6152	0.346	140	0.2178	2651	X-RAY DIFFRACTION	96
2.6152-2.6685	0.3231	162	0.2204	2631	X-RAY DIFFRACTION	96
2.6685-2.7265	0.3048	120	0.2102	2676	X-RAY DIFFRACTION	96
2.7265-2.7898	0.2876	120	0.2108	2723	X-RAY DIFFRACTION	97
2.7898-2.8595	0.2859	142	0.1964	2626	X-RAY DIFFRACTION	96
2.8595-2.9368	0.2769	155	0.1875	2677	X-RAY DIFFRACTION	97
2.9368-3.0231	0.2538	166	0.1779	2646	X-RAY DIFFRACTION	97
3.0231-3.1205	0.2591	125	0.1793	2710	X-RAY DIFFRACTION	97
3.1205-3.2318	0.2265	139	0.1733	2706	X-RAY DIFFRACTION	97
3.2318-3.361	0.2427	147	0.1733	2654	X-RAY DIFFRACTION	97
3.361-3.5136	0.2659	156	0.1745	2684	X-RAY DIFFRACTION	97
3.5136-3.6984	0.2339	164	0.173	2658	X-RAY DIFFRACTION	97
3.6984-3.9294	0.2016	140	0.1452	2685	X-RAY DIFFRACTION	97
3.9294-4.2317	0.1955	145	0.1393	2699	X-RAY DIFFRACTION	97
4.2317-4.6554	0.1772	166	0.1289	2659	X-RAY DIFFRACTION	97
4.6554-5.3242	0.1989	143	0.1407	2670	X-RAY DIFFRACTION	97
5.3242-6.6899	0.2056	147	0.1631	2691	X-RAY DIFFRACTION	97
6.6899-26.3927	0.1687	139	0.1543	2634	X-RAY DIFFRACTION	95

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	3.2837	0.2009	1.0077	2.7382	0.9943	2.1451	0.0266	-0.0471	-0.2162	0.0421	0.0642	-0.3651	0.1592	0.3163	-0.0673	0.1615	0.1055	0.0417	0.2404	0.0008	0.0893	-10.3192	-20.0517	-49.2459
2	2.3592	0.0394	0.8496	2.4776	0.8663	2.5726	0.0621	-0.0038	0.0139	0.0929	0.0094	0.1815	0.1222	-0.2128	-0.0637	0.0552	-0.0061	0.009	0.0997	0.0195	0.0419	-35.1787	-4.6068	-51.4599
3	2.2846	-1.2581	0.2434	1.2041	0.3891	0.5642	0.1089	0.301	-0.0174	-0.1664	-0.0968	-0.0146	-0.033	0.0958	-0.0173	0.1588	0.0035	0.0216	0.224	0.0139	0.0971	-24.4224	-8.3888	-57.9926
4	2.4577	-3.3045	0.0344	4.7568	-0.2994	0.2032	-0.0501	0.1389	0.6152	0.1467	0.0349	-0.8153	-0.1502	0.0609	-0.0445	0.0996	0.0023	0.0109	0.3042	-0.0065	0.2988	-10.3339	-5.8294	-50.7229
5	2.6607	-0.6268	-0.0803	1.5638	0.3804	1.8747	-0.0721	0.1517	-0.6784	0.0278	-0.0118	0.3513	0.6362	-0.1709	0.0851	0.3589	-0.0179	-0.0233	0.1376	-0.1004	0.2754	-35.8458	-31.149	-58.0054
6	1.2768	0.0047	0.3947	1.5131	0.9646	1.2919	-0.1421	0.2935	-0.2385	-0.0775	0.1086	-0.0154	0.1284	0.2106	0.0279	0.1025	0.1075	0.0901	0.191	-0.0482	0.1122	-4.7059	-20.5573	-35.1819
7	3.1064	-0.2841	-1.1132	3.301	1.4059	1.603	-0.0033	0.2995	-0.2915	-0.0219	-0.0897	0.1312	0.0588	-0.1863	0.0669	0.0813	0.0163	-0.0157	0.2234	0.0153	0.1012	-27.0676	-10.3421	-26.7616
8	6.2533	2.503	4.0544	2.6064	2.494	3.228	-0.3033	0.5703	0.4457	-0.3896	0.1252	0.0972	-0.6879	0.1968	0.1571	0.1835	0.0401	0.0181	0.1729	0.0231	0.1031	-20.0412	6.3821	-24.1297
9	1.2262	-0.78	-0.467	2.1582	1.107	2.0022	0.0001	0.0472	-0.0752	0.0918	-0.0291	-0.0151	0.092	0.0298	0.0344	0.088	0.0357	0.0075	0.1019	0.0244	0.0449	-20.6545	-7.3822	-17.8633
10	1.9718	-1.0087	-1.7876	0.6141	0.7762	1.8173	-0.1089	0.4177	-0.7408	0.0212	-0.2853	0.7891	0.1128	-0.7183	0.2464	0.2091	0.0468	0.0252	0.2893	-0.1649	0.4742	-17.6641	-24.1942	-31.388
11	1.7169	-0.0416	-0.5052	2.8644	0.11	1.6365	0.0877	-0.0063	0.1089	0.1223	0.0225	-0.187	-0.2625	0.4098	-0.1044	0.0789	-0.0215	-0.0053	0.3156	-0.0032	0.1235	1.0532	1.8916	-20.345
12	2.5247	-1.1564	-0.3938	5.0382	0.4829	3.2164	0.1565	0.2726	0.4929	-0.4428	-0.0547	-0.5484	-0.6963	0.7276	-0.0101	0.2129	-0.1238	0.0234	0.4579	0.037	0.2399	9.8039	6.6677	-22.7704
13	0.6734	-0.0367	0.3502	1.8596	0.3831	2.9308	-0.0101	-0.2454	-0.1532	0.3876	0.0241	0.0049	0.2676	0.0199	-0.0155	0.2048	0.051	0.0149	0.119	0.0494	0.1274	-20.0023	-50.1073	18.7218
14	1.7253	0.5322	0.6623	2.9818	0.6491	2.386	-0.079	0.1128	0.2694	0.1104	0.1851	-0.4421	-0.2092	0.4298	-0.1014	0.12	0.0233	0.0457	0.1249	-0.0011	0.2209	-4.0709	-29.0875	9.6427
15	1.1832	-0.5931	0.2631	1.2936	-0.143	0.3086	0.032	0.0597	0.1924	-0.23	-0.0797	-0.37	-0.2748	0.0215	0.0258	0.2481	-0.0038	0.0315	0.0862	0.044	0.1709	-21.7704	-17.2505	6.9005
16	0.7946	-0.3193	0.1568	2.1114	0.285	1.4352	0.0108	0.0011	-0.0435	-0.1506	-0.0972	0.2209	-0.0655	-0.2522	0.0222	0.1715	0.0748	-0.0284	0.0698	0.027	0.0448	-39.6028	-26.4888	5.2548
17	1.8358	-0.7284	0.2062	1.7326	-0.3438	0.5396	0.001	0.0125	0.13	-0.2188	-0.0029	-0.0874	-0.2803	-0.0538	0.0191	0.2883	0.016	0.029	0.0775	0.0129	0.1049	-22.4941	-23.0687	3.4519
18	3.2877	1.2761	0.0778	1.7298	0.5346	1.5359	0.0021	0.2669	-0.0319	-0.1731	-0.0707	0.1453	0.0576	-0.2638	0.0721	0.1594	0.0794	-0.0072	0.0435	-0.0022	0.1035	-30.6463	-45.2662	-1.1316
19	6.3824	-2.7233	-0.7329	1.1862	0.3299	0.1783	0.0823	-0.5573	-0.0382	0.3514	-0.0508	0.2607	-0.1299	0.0334	-0.0671	0.2282	-0.0581	0.0228	0.1132	-0.0078	0.1862	-29.7449	-49.4255	7.3232
20	3.469	-0.3279	-1.5954	1.8712	0.0741	2.265	-0.1547	0.236	-0.7381	-0.0024	-0.0215	0.2762	0.3921	-0.2232	0.2367	0.2267	0.0053	0.0048	0.1216	-0.0768	0.2143	-31.482	-56.4987	1.8163
21	2.9899	-0.0657	1.8504	0.4363	-0.2901	5.8421	0.0791	0.3922	0.1201	-0.3229	-0.0004	-0.594	-0.2025	0.4747	-0.0808	0.3415	-0.0138	0.1681	0.162	-0.0634	0.4836	-0.9385	-15.4511	12.3998
22	1.2755	-0.5431	-0.776	1.3571	0.6862	1.5605	-0.0175	-0.1331	0.1296	0.3008	0.0498	-0.1466	0.078	0.0597	-0.0282	0.1868	0.0004	-0.0186	0.0897	0.0034	0.0786	-20.018	-24.4986	33.3687
23	0.6126	-0.3309	-0.4482	1.4801	-0.0193	1.0756	-0.0301	-0.2907	0.3662	0.357	0.1234	-0.3197	0.112	0.1751	-0.0725	0.1557	0.0416	-0.0923	0.1497	-0.0643	0.2335	-8.9406	-29.2708	31.4149
24	1.1757	-0.1606	-0.5356	0.9797	0.1984	1.1338	0.2102	-0.0555	0.543	0.0176	0.1423	-0.6709	-0.3467	0.3514	0.0778	0.2106	-0.1415	0.0712	0.2355	-0.1806	0.6437	-0.2548	-5.3704	31.368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 37:119)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 120:239)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 240:303)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 304:341)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 342:459)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 34:106)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 107:157)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 158:196)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 197:311)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 312:341)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 342:431)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 432:459)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESSEQ 5:61)
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 62:101)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 102:141)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 142:246)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 247:327)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 328:407)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 408:427)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 428:458)
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 5:61)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 62:286)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 287:367)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 368:458)

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