PDB-4ce5: First crystal structure of an (R)-selective omega-transaminase fr...

ID or keywords:

Entry

Database: PDB / ID: 4ce5

Title

First crystal structure of an (R)-selective omega-transaminase from Aspergillus terreus

Components

AT-OMEGATA

Keywords

TRANSFERASE / AMINOTRANSFERASE / (R)-AMINE AMINOTRANSFERASE / ENANTIOSELECTIVITY / CHIRAL AMINES / TRANSAMINATION.

Function / homology

Function and homology information

aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / metal ion binding / cytosol
Similarity search - Function

Biological species

ASPERGILLUS TERREUS (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Lyskowski, A. / Gruber, C. / Steinkellner, G. / Schurmann, M. / Schwab, H. / Gruber, K. / Steiner, K.

Citation

Journal: Plos One / Year: 2014
Title: Crystal Structure of an (R)-Selective Omega-Transaminase from Aspergillus Terreus
Authors: Lyskowski, A. / Gruber, C. / Steinkellner, G. / Schurmann, M. / Schwab, H. / Gruber, K. / Steiner, K.

History

Deposition	Nov 8, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	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_sheet / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ce5.cif.gz	289.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4ce5_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4ce5_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4ce5_validation.xml.gz	39.9 KB	Display
Data in CIF	4ce5_validation.cif.gz	61 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ce/4ce5 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/4ce5	HTTPS FTP

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Related structure data

Similar structure data	6snl-3 3wwi-1 4cmd-d 2e8w-d 3wwi-5 6ss3-d 1wrv-5 3wwj-4 3ht5-1 3wwh-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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (5)

Deposited unit

A: AT-OMEGATA

B: AT-OMEGATA

hetero molecules

76.2 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)	105.670, 135.310, 116.410
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

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Protein , 1 types, 2 molecules AB

#1: Protein	AT-OMEGATA / OMEGA-TRANSAMINASE Mass: 37279.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ACTIVE SITE INTERPRETED AS TWO DISTINCT STATES, (I) FREE LYS180 AND PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE (PDG) AND (II) LYSINE-BOUND PYRIDOXAL-5'-PHOSPHATE (PLP) Source: (gene. exp.) ASPERGILLUS TERREUS (mold) / Strain: NIH 2624 / FGSC A1156 / Plasmid: PET28A-AT-OMEGATA-CHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / TOP10F' References: UniProt: Q0C8G1, branched-chain-amino-acid transaminase

#1: Protein

AT-OMEGATA / OMEGA-TRANSAMINASE

Mass: 37279.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACTIVE SITE INTERPRETED AS TWO DISTINCT STATES, (I) FREE LYS180 AND PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE (PDG) AND (II) LYSINE-BOUND PYRIDOXAL-5'-PHOSPHATE (PLP)
Source: (gene. exp.)

ASPERGILLUS TERREUS (mold) / Strain: NIH 2624 / FGSC A1156 / Plasmid: PET28A-AT-OMEGATA-CHIS / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / TOP10F'
References: UniProt: Q0C8G1, branched-chain-amino-acid transaminase

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Non-polymers , 5 types, 1118 molecules

#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: Chemical	ChemComp-PDG / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID / N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₉N₂O₉P
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1103 / 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: 2.88 Å³/Da / Density % sol: 57.26 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9793
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.63→41.64 Å / Num. obs: 103737 / % possible obs: 100 % / Observed criterion σ(I): 2.99 / Redundancy: 7.43 % / B_iso Wilson estimate: 13.12 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 19.47
Reflection shell	Resolution: 1.63→1.69 Å / Redundancy: 7.43 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 2.99 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
xia2		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ENSEMBLE OF SELECTED HOMOLOGOUS PROTEINS

Resolution: 1.63→41.483 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 14.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1669	5186	5 %
R_work	0.1371	-	-
obs	0.1386	103727	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.63→41.483 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5088	0	91	1103	6282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5306
X-RAY DIFFRACTION	f_angle_d	1.074	7218
X-RAY DIFFRACTION	f_dihedral_angle_d	12.441	1944
X-RAY DIFFRACTION	f_chiral_restr	0.047	790
X-RAY DIFFRACTION	f_plane_restr	0.006	932

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 (%)
1.63-1.6485	0.2252	181	0.1952	3279	X-RAY DIFFRACTION	100
1.6485-1.6679	0.2243	158	0.1902	3231	X-RAY DIFFRACTION	100
1.6679-1.6883	0.2213	172	0.1787	3281	X-RAY DIFFRACTION	100
1.6883-1.7096	0.229	155	0.1793	3253	X-RAY DIFFRACTION	100
1.7096-1.7321	0.2047	157	0.1731	3271	X-RAY DIFFRACTION	100
1.7321-1.7559	0.1979	199	0.1608	3235	X-RAY DIFFRACTION	100
1.7559-1.7809	0.1876	160	0.1613	3247	X-RAY DIFFRACTION	100
1.7809-1.8075	0.2032	191	0.1649	3263	X-RAY DIFFRACTION	100
1.8075-1.8358	0.2105	184	0.164	3236	X-RAY DIFFRACTION	100
1.8358-1.8659	0.2091	182	0.1555	3254	X-RAY DIFFRACTION	100
1.8659-1.898	0.1919	190	0.1569	3241	X-RAY DIFFRACTION	100
1.898-1.9326	0.1769	160	0.1545	3267	X-RAY DIFFRACTION	100
1.9326-1.9697	0.1743	175	0.1385	3262	X-RAY DIFFRACTION	100
1.9697-2.0099	0.1485	166	0.1335	3285	X-RAY DIFFRACTION	100
2.0099-2.0536	0.1467	177	0.122	3250	X-RAY DIFFRACTION	100
2.0536-2.1014	0.1623	161	0.1308	3314	X-RAY DIFFRACTION	100
2.1014-2.154	0.1654	177	0.1325	3251	X-RAY DIFFRACTION	100
2.154-2.2122	0.1409	202	0.1292	3232	X-RAY DIFFRACTION	100
2.2122-2.2773	0.1753	190	0.1273	3256	X-RAY DIFFRACTION	100
2.2773-2.3508	0.1492	175	0.1333	3273	X-RAY DIFFRACTION	100
2.3508-2.4348	0.1744	147	0.1329	3311	X-RAY DIFFRACTION	100
2.4348-2.5323	0.1521	150	0.136	3335	X-RAY DIFFRACTION	100
2.5323-2.6475	0.164	168	0.1401	3266	X-RAY DIFFRACTION	100
2.6475-2.787	0.1521	153	0.1346	3332	X-RAY DIFFRACTION	100
2.787-2.9616	0.1801	180	0.1398	3306	X-RAY DIFFRACTION	100
2.9616-3.1902	0.1825	173	0.1311	3301	X-RAY DIFFRACTION	100
3.1902-3.5111	0.1554	183	0.1293	3302	X-RAY DIFFRACTION	100
3.5111-4.0188	0.1535	175	0.1242	3351	X-RAY DIFFRACTION	100
4.0188-5.0619	0.1214	176	0.1071	3370	X-RAY DIFFRACTION	100
5.0619-41.496	0.167	169	0.1378	3486	X-RAY DIFFRACTION	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	0.4839	-0.2015	0.0722	0.9806	-0.494	0.9495	0.0132	0.0248	-0.0081	-0.0491	-0.0927	-0.2374	0.1334	0.2149	0.0397	0.1129	0.0426	0.0111	0.1271	0.0073	0.1518	-20.9038	-56.7338	27.2062
2	1.971	-0.43	-0.0203	1.9235	-0.0112	0.6458	0.0579	0.2801	0.1031	-0.3016	-0.0983	-0.0982	0.0782	0.2113	0.0021	0.1145	0.0241	0.028	0.1056	0.0051	0.1206	-25.1037	-49.5344	17.2904
3	0.3588	-0.2047	0.0962	0.9965	-0.0559	0.4857	0.0073	-0.0274	-0.0416	0.0253	-0.0019	0.0237	0.0724	-0.0163	-0.0086	0.0886	0.0039	-0.006	0.1019	0.0067	0.0877	-40.4305	-52.3465	38.6097
4	1.2876	-0.8662	-0.5851	1.8756	0.605	1.3836	-0.0007	-0.0762	-0.0619	0.0559	0.0066	-0.0911	0.179	0.079	-0.0001	0.1151	0.015	-0.0317	0.0899	0.0126	0.09	-31.1994	-62.5568	42.339
5	0.3358	0.064	-0.0577	0.6919	-0.6893	1.0856	0.0034	-0.0041	0.0184	-0.0503	-0.0678	-0.1365	0.011	0.1421	0.0567	0.0747	-0.0089	0.0112	0.0961	0.0023	0.1108	-23.6732	-25.0909	16.1885
6	1.2617	-0.105	0.119	2.211	-1.109	2.6958	0.0244	-0.1737	-0.0714	0.1917	-0.0777	-0.1864	-0.0345	0.2652	0.0741	0.0659	-0.003	-0.0093	0.1094	0.0144	0.1117	-22.8273	-32.3059	26.966
7	0.5318	0.3055	-0.0405	0.8954	-0.2127	0.5458	-0.0236	0.036	0.0807	-0.0495	0.0383	0.0679	-0.013	-0.0334	-0.0151	0.0757	-0.0016	-0.0034	0.1064	0.0051	0.0902	-46.2027	-29.4924	14.9731
8	1.2292	0.7582	0.201	1.4333	0.0087	0.8859	-0.0623	0.0924	0.1019	-0.1759	0.0809	0.0163	-0.0483	-0.0176	-0.0223	0.0923	-0.0042	0.0107	0.0811	0.0125	0.0707	-39.3471	-19.2432	7.3889

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1 THROUGH 111 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 112 THROUGH 145 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 146 THROUGH 267 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 268 THROUGH 325 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 1 THROUGH 111 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 112 THROUGH 145 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 146 THROUGH 267 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 268 THROUGH 325 )

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