PDB-4a6u: Crystal structure of the omega transaminase from Chromobacterium ...

ID or keywords:

Entry

Database: PDB / ID: 4a6u

Title

Crystal structure of the omega transaminase from Chromobacterium violaceum in the apo form, crystallised from PEG 3350

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: 1.687 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 8, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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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PDBx/mmCIF format	4a6u.cif.gz	328.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4a6u_validation.pdf.gz	443.9 KB	Display	wwPDB validaton report
Full document	4a6u_full_validation.pdf.gz	448.5 KB	Display
Data in XML	4a6u_validation.xml.gz	34.2 KB	Display
Data in CIF	4a6u_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6u ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6u	HTTPS FTP

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Related structure data

Related structure data	4a6rSC 4a6tC 4a72C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4a72-1 4a6r-d 4ba4-d 6hx9-d 5ti8-d 5l6m-2 4aja-1 1ika-1 5l6m-1 2vzs-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
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: OMEGA TRANSAMINASE

B: OMEGA TRANSAMINASE

hetero molecules

103 kDa, 2 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)	57.170, 61.110, 60.240
Angle α, β, γ (deg.)	109.14, 85.59, 103.25
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.9974, -0.0541, 0.0472), (-0.06423, 0.3787, -0.9233), (0.03207, -0.924, -0.3812)
Vector: 45.1, -30.41, -48.34)

#1: Protein	OMEGA TRANSAMINASE / PROBABLE AMINOTRANSFERASE Mass: 51279.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	SODIUM ION (NA): ASSIGNED BASED ON COORDINATION DISTANCE ONLY

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.88 Å³/Da / Density % sol: 34.6 % / Description: NONE
Crystal grow	pH: 7.4 Details: 200 NL OF PROTEIN AT 12 MG/ML MIXED WITH 200NL OF 20 % W/V PEG 3350, 0.2 M NASCN, 0.1 M HEPES PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04002
Detector	Type: MARRESEARCH SX-165 / Detector: CCD / Date: May 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: 1.04002 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. obs: 78926 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / B_iso Wilson estimate: 12.34 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 2 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 3.1 / % possible all: 72.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6R

4a6r

Resolution: 1.687→29.473 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 17.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1799	3888	4.9 %
R_work	0.1545	-	-
obs	0.1557	78922	93.58 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.801 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.0967 Å²	-0.6546 Å²	-2.1588 Å²
2-	-	-2.7565 Å²	1.0691 Å²
3-	-	-	-0.3402 Å²

Refinement step

Cycle: LAST / Resolution: 1.687→29.473 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6154	0	11	617	6782

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6420
X-RAY DIFFRACTION	f_angle_d	1.116	8700
X-RAY DIFFRACTION	f_dihedral_angle_d	13.356	2367
X-RAY DIFFRACTION	f_chiral_restr	0.067	922
X-RAY DIFFRACTION	f_plane_restr	0.007	1133

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 (%)
1.6872-1.7078	0.2576	80	0.2899	1434	X-RAY DIFFRACTION	51
1.7078-1.7294	0.2821	140	0.2373	2665	X-RAY DIFFRACTION	92
1.7294-1.7522	0.2307	132	0.2006	2636	X-RAY DIFFRACTION	92
1.7522-1.7762	0.1956	137	0.1964	2677	X-RAY DIFFRACTION	94
1.7762-1.8016	0.2199	139	0.1922	2684	X-RAY DIFFRACTION	93
1.8016-1.8285	0.2301	133	0.1897	2699	X-RAY DIFFRACTION	94
1.8285-1.857	0.2279	168	0.1916	2661	X-RAY DIFFRACTION	95
1.857-1.8875	0.2323	147	0.1833	2704	X-RAY DIFFRACTION	94
1.8875-1.92	0.1685	144	0.1667	2716	X-RAY DIFFRACTION	95
1.92-1.9549	0.1974	123	0.1568	2757	X-RAY DIFFRACTION	95
1.9549-1.9925	0.2002	141	0.1511	2674	X-RAY DIFFRACTION	95
1.9925-2.0332	0.1797	139	0.1517	2757	X-RAY DIFFRACTION	95
2.0332-2.0774	0.1769	133	0.1435	2717	X-RAY DIFFRACTION	95
2.0774-2.1257	0.1679	141	0.1429	2735	X-RAY DIFFRACTION	95
2.1257-2.1788	0.1814	125	0.1383	2756	X-RAY DIFFRACTION	95
2.1788-2.2377	0.1646	122	0.1414	2761	X-RAY DIFFRACTION	96
2.2377-2.3035	0.1856	154	0.143	2728	X-RAY DIFFRACTION	96
2.3035-2.3778	0.1545	139	0.1355	2746	X-RAY DIFFRACTION	96
2.3778-2.4628	0.1772	138	0.1364	2763	X-RAY DIFFRACTION	96
2.4628-2.5613	0.1641	145	0.1415	2736	X-RAY DIFFRACTION	96
2.5613-2.6778	0.1743	141	0.1477	2781	X-RAY DIFFRACTION	96
2.6778-2.8189	0.1651	150	0.1464	2757	X-RAY DIFFRACTION	96
2.8189-2.9954	0.1974	152	0.1529	2781	X-RAY DIFFRACTION	97
2.9954-3.2264	0.1965	116	0.1525	2802	X-RAY DIFFRACTION	97
3.2264-3.5506	0.169	159	0.1548	2766	X-RAY DIFFRACTION	97
3.5506-4.0632	0.1577	157	0.138	2739	X-RAY DIFFRACTION	96
4.0632-5.1149	0.1405	148	0.1304	2699	X-RAY DIFFRACTION	95
5.1149-29.4775	0.1836	145	0.1797	2703	X-RAY DIFFRACTION	94

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	1.327	-0.7998	0.4925	1.4976	-0.1557	1.0333	-0.0833	-0.0851	0.1241	0.1352	0.0405	0.175	-0.082	-0.1011	0.0377	0.0388	0.0096	0.0061	0.0292	-0.0022	0.1459	26.2606	7.9036	-16.7731
2	2.1779	1.1588	1.1595	0.8075	0.727	1.5745	-0.0857	0.3547	-0.0995	-0.1933	0.1008	-0.0076	-0.0701	0.1278	-0.0029	0.0749	-0.0316	0.0222	0.1368	0.0186	0.0755	29.4324	-7.0781	-40.2037
3	0.3994	-0.8038	0.4516	2.7107	-0.6441	0.8291	0.0391	0.093	-0.1716	-0.2451	0.0244	0.0584	0.1937	0.0381	-0.0616	0.0829	0.0146	-0.0111	0.0575	-0.0075	0.0852	34.5557	-22.105	-26.397
4	0.593	0.5008	0.7458	3.1974	1.4677	1.7302	-0.0807	-0.1257	-0.0293	0.1391	-0.0403	0.1599	0.0354	-0.0612	0.0955	0.0655	0.0307	0.039	0.0635	-0.0049	0.0699	40.7543	-24.0126	-4.8761
5	0.3026	-0.4555	0.0566	1.022	-0.4621	0.4996	-0.0217	-0.0249	0.0183	0.0389	-0.0088	0.0033	0.0294	0.055	0.0184	0.0331	0.0317	0.0051	0.0273	-0.0197	0.0994	42.1736	-17.0045	-15.4541
6	2.1171	-1.6305	0.0457	4.0373	-0.1889	0.9207	0.0456	0.2072	-0.2437	-0.2757	-0.0493	0.0969	0.2231	0.1004	0.0076	0.07	0.0285	0.0135	0.0504	-0.0188	0.0753	35.0844	-17.3882	-29.6525
7	0.685	0.0638	0.4099	0.6668	0.0584	1.0903	-0.0269	-0.1172	0.1127	0.1642	0.0428	0.0224	-0.1015	-0.0492	-0.0248	0.0574	0.0115	0.0068	0.0486	-0.0138	0.0755	36.0319	2.5401	-5.0985
8	0.7946	0.5698	0.4369	0.8453	0.328	0.7544	-0.096	0.136	0.1467	-0.1645	0.0705	0.0099	-0.1033	0.0302	-0.0102	0.0459	-0.0065	-0.0147	0.0916	0.0533	0.1024	16.0813	-5.277	-36.4073
9	0.4281	0.8006	-0.5617	1.6669	-1.2214	1.9226	0.1139	-0.2519	-0.0054	0.2254	-0.1638	-0.0735	-0.0362	0.0582	0.0574	0.0851	-0.0298	-0.0117	0.1064	0.0036	0.0818	10.6867	-16.7461	-16.5502
10	0.4303	0.4798	-0.4277	1.3592	-0.4765	0.6516	-0.0099	0.0102	-0.024	0.0435	-0.0287	-0.0374	0.0697	0.0885	0.016	0.0281	0.0003	-0.0079	0.0669	0.0052	0.0326	4.257	-30.7326	-24.1605
11	2.7873	1.1773	-1.7278	2.2558	-1.3805	2.8529	0.1311	-0.3506	0.1698	0.3949	-0.0584	0.1586	-0.1868	0.1357	-0.0508	0.0576	-0.0069	0.0159	0.0919	0.0088	0.0713	10.2937	-11.0156	-20.2437
12	0.5726	0.6887	0.3379	1.1432	0.1114	0.616	-0.1479	0.2489	-0.0184	-0.3951	0.1501	-0.0974	0.0918	0.0621	-0.0234	0.1132	-0.0313	-0.0089	0.1401	0.0045	0.0101	8.8928	-27.1879	-47.6635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 34:68)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 69:105)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 106:137)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 138:215)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 216:291)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 292:325)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 326:459)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 34:105)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 106:137)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 138:291)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 292:325)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 326:459)

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