PDB-7lom: Ornithine Aminotransferase (OAT) soaked with its inactivator - (1...

ID or keywords:

Entry

Database: PDB / ID: 7lom

Title

Ornithine Aminotransferase (OAT) soaked with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid

Components

Ornithine aminotransferase, mitochondrial

Keywords

TRANSFERASE/Inactivator / Ornithine Aminotransferase / OAT / aminotransferase / inactivator / inhibitor / TRANSFERASE / TRANSFERASE-Inactivator complex

Function / homology

Function and homology information

arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Butrin, A. / Zhu, W. / Liu, D. / Silverman, R.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2021
Title: Remarkable and Unexpected Mechanism for ( S )-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase.
Authors: Zhu, W. / Doubleday, P.F. / Butrin, A. / Weerawarna, P.M. / Melani, R.D. / Catlin, D.S. / Dwight, T.A. / Liu, D. / Kelleher, N.L. / Silverman, R.B.

History

Deposition	Feb 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 25, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	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	7lom.cif.gz	491.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7lom.ent.gz	407.5 KB	Display	PDB format
PDBx/mmJSON format	7lom.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7lom_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7lom_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7lom_validation.xml.gz	49.2 KB	Display
Data in CIF	7lom_validation.cif.gz	68.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lo/7lom ftp://data.pdbj.org/pub/pdb/validation_reports/lo/7lom	HTTPS FTP

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Related structure data

Related structure data	7lnmC 7lonC 1oatS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2can-1 7lnm-2 1oat-1 6v8c-1 6oia-2 2byj-1 2byl-2 7nnc-1 1gbn-3 6hx7-1 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: Ornithine aminotransferase, mitochondrial

B: Ornithine aminotransferase, mitochondrial

C: Ornithine aminotransferase, mitochondrial

hetero molecules

136 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine aminotransferase, mitochondrial

hetero molecules

A: Ornithine aminotransferase, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration
90.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ornithine aminotransferase, mitochondrial

hetero molecules

C: Ornithine aminotransferase, mitochondrial

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.610, 115.610, 186.570
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-670- HOH
2	1	A-757- HOH
3	1	C-772- HOH

#1: Protein	Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase Mass: 44860.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical	ChemComp-THR / THREONINE Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₉NO₃
#3: Chemical	ChemComp-Y8P / (3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid Mass: 388.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₅N₂O₇P
#4: Chemical	ChemComp-YCD / (4~{R})-4-(fluoranylmethyl)-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid Mass: 400.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₁₈FN₂O₇P
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.66 Å³/Da / Density % sol: 53.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition ...Details: The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition contained 8% PEG 6000, 100 mM NaCl, 5% glycerol, and 50 mM Tricine pH 7.8. Once the holoenzyme crystals reached their maximum size within five days, 1 uL of 10 mM 181 was added to the drop with crystals. Within the first three minutes of 181 addition, the hOAT crystals turned their color from yellow to transparent. The crystals were soaked for 44 minutes, transferred into cryoprotective solution (well solution supplemented with 30% glycerol), and then flash-frozen in liquid nitrogen.

Crystal

Density Matthews: 2.66 Å³/Da / Density % sol: 53.79 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: The holoenzyme crystals were first grown via a hanging drop vapor diffusion method. Each drop contained 2 uL of protein and 2 uL of well solution. The best crystallization condition ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.1271 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 19, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.1271 Å / Relative weight: 1

Reflection

Resolution: 2.1→44.11 Å / Num. obs: 83376 / % possible obs: 98.4 % / Redundancy: 7 % / B_iso Wilson estimate: 34.37 Å² / R_pim(I) all: 0.065 / R_rim(I) all: 0.175 / Net I/σ(I): 7.3 / Num. measured all: 579510

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	% possible all
2.1-2.14	7.1	0.9	29842	4194	0.825	2.235	99.8
5.7-44.12	7.3	22.8	31303	4278	0.025	0.071	94.8

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
xia2		data scaling
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat

Resolution: 2.1→44.11 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.235	4098	4.92 %
R_work	0.2	-	-
obs	0.201	83345	98.4 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→44.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9450	0	100	470	10020

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 (%)
2.1-2.12	0.3491	132	0.3357	2771	X-RAY DIFFRACTION	100
2.12-2.15	0.3186	159	0.3177	2693	X-RAY DIFFRACTION	100
2.15-2.18	0.3402	132	0.3088	2750	X-RAY DIFFRACTION	100
2.18-2.21	0.3215	130	0.2979	2742	X-RAY DIFFRACTION	99
2.21-2.24	0.3171	127	0.292	2753	X-RAY DIFFRACTION	99
2.24-2.27	0.314	151	0.2882	2726	X-RAY DIFFRACTION	100
2.27-2.3	0.3051	171	0.2777	2724	X-RAY DIFFRACTION	99
2.3-2.34	0.2959	131	0.2787	2703	X-RAY DIFFRACTION	99
2.34-2.38	0.2667	125	0.2602	2759	X-RAY DIFFRACTION	100
2.38-2.42	0.3025	138	0.2592	2739	X-RAY DIFFRACTION	99
2.42-2.46	0.2674	138	0.2504	2742	X-RAY DIFFRACTION	99
2.46-2.51	0.2928	165	0.2388	2718	X-RAY DIFFRACTION	99
2.51-2.56	0.2841	158	0.2405	2713	X-RAY DIFFRACTION	99
2.56-2.62	0.2766	148	0.2419	2702	X-RAY DIFFRACTION	99
2.62-2.68	0.2466	153	0.2347	2742	X-RAY DIFFRACTION	99
2.68-2.74	0.282	147	0.2187	2710	X-RAY DIFFRACTION	99
2.74-2.82	0.2587	144	0.2139	2734	X-RAY DIFFRACTION	99
2.82-2.9	0.27	128	0.2154	2721	X-RAY DIFFRACTION	99
2.9-2.99	0.2576	123	0.2182	2742	X-RAY DIFFRACTION	99
2.99-3.1	0.2531	158	0.2138	2727	X-RAY DIFFRACTION	98
3.1-3.23	0.2271	137	0.2032	2766	X-RAY DIFFRACTION	98
3.23-3.37	0.2572	137	0.1992	2712	X-RAY DIFFRACTION	98
3.37-3.55	0.2154	111	0.1892	2737	X-RAY DIFFRACTION	98
3.55-3.77	0.1902	97	0.1749	2761	X-RAY DIFFRACTION	97
3.77-4.06	0.2287	136	0.1588	2721	X-RAY DIFFRACTION	97
4.06-4.47	0.1932	166	0.1547	2701	X-RAY DIFFRACTION	97
4.47-5.12	0.1822	173	0.1559	2672	X-RAY DIFFRACTION	96
5.12-6.45	0.2395	122	0.1829	2779	X-RAY DIFFRACTION	96
6.45-44.11	0.1834	161	0.1585	2787	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	0.0138	0.0379	0.0461	0.257	0.3728	0.5967	0.1135	1.0044	-0.027	-0.2191	0.2259	0.4321	-0.3879	-0.4739	-0.2891	0.3642	0.0517	-0.0763	0.8207	0.2027	1.0195	-6.9524	-13.1446	-50.137
2	1.7343	0.512	-0.3863	0.6286	0.035	1.3526	0.1915	0.1635	0.5351	0.0961	0.0493	0.3783	-0.56	-0.542	-0.1926	0.4795	0.1347	0.1402	0.4681	0.1381	1.1654	-7.7291	-3.6626	-30.5824
3	1.1111	0.5346	-0.478	0.5837	-0.1219	1.1061	0.0913	-0.0336	0.1517	0.0898	-0.0395	0.17	-0.0972	-0.0741	-0.0425	0.2461	-0.0684	0.0636	0.3279	-0.0187	0.5108	8.0004	-24.5853	-21.4841
4	1.376	-0.4398	0.5105	2.3343	-0.4338	1.3611	0.0643	-0.0021	0.3044	0.1904	0.0035	0.4231	-0.1086	-0.2535	-0.0716	0.2795	-0.0688	0.1143	0.39	-0.0297	0.5898	-1.7564	-26.448	-15.2802
5	3.4721	-0.1075	0.3737	1.1844	-0.4036	1.8806	0.191	-0.0636	0.1637	0.1842	0.0418	0.5403	-0.1322	-0.4632	-0.1562	0.2524	-0.0084	0.1124	0.3833	0.0376	0.7654	-8.1381	-17.343	-23.7105
6	0.6001	0.2779	0.6407	0.3302	0.0296	1.014	-0.0263	0.2707	0.13	-0.0541	0.216	0.7156	-0.1362	-0.8175	0.2776	-0.0296	0.0054	0.0689	1.028	0.2793	1.1748	-21.9813	-20.0202	-34.8944
7	1.8788	-0.6224	-0.7965	0.2347	0.2591	0.3593	0.0466	0.4702	0.4159	-0.4756	-0.0474	0.0035	-0.2762	0.4444	-0.1373	0.5899	-0.077	-0.01	0.5753	0.1108	0.6973	3.0445	-43.1139	-97.2476
8	2.0881	0.2105	-0.0009	1.6068	0.0865	4.2201	0.0746	-0.0979	0.4316	-0.2412	-0.0609	-0.4221	-0.4644	0.7348	-0.1245	0.5706	-0.2859	0.056	0.6676	-0.0048	0.6262	16.0434	-40.7689	-85.9445
9	2.0955	0.6917	-0.263	2.898	0.6574	2.1184	-0.0463	-0.1419	-0.0007	0.2283	0.1442	-0.17	-0.4952	0.7069	-0.1291	0.3217	-0.1205	-0.0442	0.7583	0.039	0.4423	16.6552	-56.035	-80.2091
10	0.515	0.1958	-0.4892	1.1196	0.0932	1.6081	0.0159	-0.1165	-0.189	-0.003	-0.0054	-0.046	-0.0248	0.321	-0.0078	0.2121	0.0513	-0.0543	0.4826	0.0421	0.3507	-1.9008	-66.9961	-71.7501
11	1.0915	0.207	-0.3932	1.4972	-0.2533	2.0994	0.1153	-0.0902	0.1299	0.1079	-0.0119	0.2452	-0.3264	-0.0408	-0.0786	0.3291	0.0391	0.0023	0.3777	-0.019	0.3824	-12.1962	-53.3858	-65.87
12	1.3094	-0.2416	-0.1058	1.336	-0.2464	1.5875	0.1212	-0.2072	-0.1904	0.0859	-0.0538	-0.2686	-0.0522	0.5596	-0.069	0.2297	-0.0161	-0.0468	0.5338	0.009	0.3428	5.6238	-60.6237	-70.1775
13	2.6128	1.7903	-0.6574	4.4416	0.4331	3.2843	0.1636	-0.4106	1.0892	0.669	0.1775	0.2432	-0.8596	0.5693	-0.1321	0.7217	-0.288	0.0919	0.5675	-0.1093	0.674	7.09	-35.2214	-66.3178
14	0.8462	-1.1252	1.3005	5.5537	-1.0398	5.8346	0.1179	-0.2479	0.8167	-0.2531	0.2752	0.5021	-1.2748	0.114	-0.2035	0.8731	-0.0963	0.0243	0.4806	0.0357	0.9379	0.6492	-28.1465	-82.2089
15	2.333	-2.3277	1.5457	5.768	-1.4356	5.0268	0.0479	-0.213	0.7986	0.1551	-0.0262	-0.349	-1.0001	0.3056	-0.0446	0.5826	-0.2946	0.0852	0.6222	-0.1067	0.7553	9.8177	-34.2023	-75.4471
16	0.0409	0.0199	0.0154	0.1307	0.0204	0.0075	-0.0006	-0.4484	-0.0719	0.0268	-0.0277	0.358	0.4811	-0.4162	0.0021	0.4512	-0.19	0.1275	0.5281	0.034	0.6381	-16.4871	-67.7967	-9.9132
17	1.4383	-0.6438	0.4203	0.7341	0.0538	1.1402	0.1847	-0.2822	-0.1653	0.0208	-0.0974	0.4384	0.2477	-0.3282	-0.0248	0.5071	-0.2594	0.0093	0.4752	0.0257	0.6505	-15.0044	-75.335	-28.3855
18	1.1045	0.2679	0.0691	2.0893	0.0525	2.0545	-0.0211	0.06	-0.1555	-0.0203	-0.068	-0.2173	0.4316	0.1428	0.0577	0.3215	-0.0423	0.0484	0.3433	0.0047	0.3682	11.693	-66.1183	-30.8485
19	0.0203	-0.028	0.2077	1.26	-0.4729	1.9848	0.0256	0.0068	0.0892	0.036	0.0567	-0.0111	-0.0203	-0.1859	0.0675	0.2299	-0.0942	0.0089	0.2864	0.0173	0.3713	5.198	-47.1245	-25.483
20	3.5963	0.3877	0.4272	2.2097	-0.111	1.1143	-0.1507	0.175	-0.0692	-0.2363	0.0518	0.0299	-0.0059	0.024	0.0484	0.3561	-0.1115	-0.0033	0.3442	0.0213	0.3814	5.4131	-50.566	-37.9604
21	2.6786	0.2427	0.69	2.3681	-0.4357	1.2359	-0.0263	0.3513	-0.0354	-0.2399	0.0475	0.0927	-0.0818	-0.1075	-0.0271	0.3686	-0.1224	0.0009	0.3374	-0.0221	0.3261	-0.4414	-62.5193	-39.7791
22	2.2288	0.0328	-0.0162	1.9983	-0.2697	1.0588	0.0435	0.1404	-0.1883	-0.224	0.0369	0.1479	0.3392	-0.1322	-0.0469	0.4065	-0.1347	0.0329	0.3419	-0.0092	0.2988	-0.7684	-68.7168	-35.6576
23	2.3068	0.8456	1.0605	2.681	-0.5397	1.9698	0.1161	-0.2419	0.6185	0.5298	-0.1474	0.8264	-0.1292	-0.5747	-0.0703	0.3787	-0.0952	0.1067	0.561	-0.0043	1.0318	-21.3303	-49.7186	-30.8447
24	2.2698	-1.9827	-2.4927	2.3373	1.2039	5.3655	0.0682	0.0282	0.1639	-0.012	0.0194	0.4369	-0.1311	-0.3235	-0.0967	0.3103	-0.1964	0.0179	0.5463	0.0725	0.6957	-23.5061	-60.4373	-29.8966

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 37 THROUGH 61 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 62 THROUGH 117 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 118 THROUGH 220 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 221 THROUGH 290 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 291 THROUGH 389 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 390 THROUGH 439 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 37 THROUGH 61 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 62 THROUGH 82 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 83 THROUGH 106 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 107 THROUGH 181 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 182 THROUGH 263 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 264 THROUGH 344 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 345 THROUGH 381 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 382 THROUGH 400 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 401 THROUGH 439 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 37 THROUGH 61 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 62 THROUGH 105 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 106 THROUGH 181 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 182 THROUGH 220 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 221 THROUGH 263 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 264 THROUGH 295 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 296 THROUGH 362 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 363 THROUGH 389 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 390 THROUGH 439 )

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