PDB-5dwn: Crystal structure of Phosphinothricin N-acetyltransferase from Br...

ID or keywords:

Entry

Database: PDB / ID: 5dwn

Title

Crystal structure of Phosphinothricin N-acetyltransferase from Brucella ovis in complex with AcetylCoA

Components

Phosphinothricin N-acetyltransferase

Keywords

TRANSFERASE / SSGCID / Brucella ovis / brucellosis / Phosphinothricin N-acetyltransferase / AcetylCoA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function

Biological species

Brucella ovis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Phosphinothricin N-acetyltransferase from Brucella ovis in complex with AcetylCoA
Authors: Abendroth, J. / Clifton, M.C. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Sep 22, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dwn.cif.gz	309.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5dwn.ent.gz	251.7 KB	Display	PDB format
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Validation report

Summary document	5dwn_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5dwn_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5dwn_validation.xml.gz	34.3 KB	Display
Data in CIF	5dwn_validation.cif.gz	49.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dw/5dwn ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dwn	HTTPS FTP

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Related structure data

Similar structure data	5dwm-2 5dwm-1 5wip-1 6z15-1 1yvo-d 7mjb-d 2j8r-d 6ysb-1 4u74-2 6ubp-2 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
Other databases	TargetTrack: SSGCID-BrovA.17352.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: Phosphinothricin N-acetyltransferase

B: Phosphinothricin N-acetyltransferase

C: Phosphinothricin N-acetyltransferase

D: Phosphinothricin N-acetyltransferase

hetero molecules

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

1

A: Phosphinothricin N-acetyltransferase

D: Phosphinothricin N-acetyltransferase

hetero molecules

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

2

B: Phosphinothricin N-acetyltransferase

C: Phosphinothricin N-acetyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.100, 77.380, 135.840
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Phosphinothricin N-acetyltransferase Mass: 20590.475 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria) Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: pat, BOV_0087 / Plasmid: BrovA.17352.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A0H3AQB6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.27 Å³/Da / Density % sol: 46 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Microlytics screen MCSG1, b9: 200mM MgCl2, 20% PEG 3350; BrovA.17352.a.B1.PS02313 at 4mg/ml, supplemented with 5mM NAD; cryo: 20% EG with 5mM AcCoA; tray 262506 b9; puck jbj3-8

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 16, 2015

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 55358 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / B_iso Wilson estimate: 22.7 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.067 / R_rim(I) all: 0.072 / Χ²: 0.963 / Net I/σ(I): 22.42 / Num. measured all: 409137

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.95-2		7.4	0.913	0.465	4.46	30122	4045	4044	0.499	100
2-2.06			0.942	0.377	5.48	29392	3936	3936	0.405	100
2.06-2.12			0.965	0.293	6.97	28607	3830	3830	0.315	100
2.12-2.18			0.977	0.237	8.51	27840	3723	3720	0.254	99.9
2.18-2.25			0.982	0.202	9.85	26987	3613	3612	0.217	100
2.25-2.33			0.985	0.185	10.67	26061	3496	3493	0.199	99.9
2.33-2.42			0.99	0.145	13.63	25391	3393	3393	0.156	100
2.42-2.52			0.993	0.127	15.09	24394	3269	3269	0.137	100
2.52-2.63			0.995	0.107	17.77	23356	3131	3129	0.115	99.9
2.63-2.76			0.996	0.086	21.49	22422	3001	3001	0.093	100
2.76-2.91			0.997	0.075	24.25	21221	2850	2849	0.081	100
2.91-3.08			0.998	0.059	29.99	20223	2725	2724	0.064	100
3.08-3.3			0.998	0.047	37.55	18717	2537	2535	0.05	99.9
3.3-3.56			0.999	0.039	43.28	17615	2402	2400	0.042	99.9
3.56-3.9			0.999	0.035	48.04	16085	2207	2206	0.038	100
3.9-4.36			0.999	0.03	54.18	14459	2000	1999	0.032	99.9
4.36-5.03			0.999	0.027	56.88	12820	1791	1791	0.029	100
5.03-6.17			0.999	0.029	52.96	10809	1523	1523	0.032	100
6.17-8.72			1	0.026	54.87	8348	1209	1208	0.028	99.9
	8.72		0.999	0.024	60.16	4268	711	696	0.026	97.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2 Å	48.85 Å
Translation	2 Å	48.85 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building
PHENIX	1.10_2155	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: native structure

Resolution: 1.95→48.852 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1968	1994	3.6 %	Random selection
R_work	0.1564	53354	-	-
obs	0.1578	55348	99.93 %	-

Solvent computation

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

Displacement parameters

B_iso max: 82.61 Å² / B_iso mean: 29.481 Å² / B_iso min: 8.76 Å²

Refinement step

Cycle: final / Resolution: 1.95→48.852 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5460	0	206	596	6262
B_iso mean	-	-	36.92	35.42	-
Num. residues	-	-	-	-	718

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5924
X-RAY DIFFRACTION	f_angle_d	0.806	8099
X-RAY DIFFRACTION	f_chiral_restr	0.053	877
X-RAY DIFFRACTION	f_plane_restr	0.005	1099
X-RAY DIFFRACTION	f_dihedral_angle_d	14.581	3568

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.95-1.9988	0.2746	129	0.1953	3770	3899
1.9988-2.0528	0.2378	167	0.1792	3726	3893
2.0528-2.1132	0.2188	117	0.1683	3788	3905
2.1132-2.1814	0.2137	139	0.1617	3757	3896
2.1814-2.2594	0.217	152	0.1619	3765	3917
2.2594-2.3499	0.209	139	0.1597	3772	3911
2.3499-2.4568	0.2043	136	0.1549	3797	3933
2.4568-2.5863	0.2144	147	0.1671	3771	3918
2.5863-2.7483	0.2125	143	0.1611	3811	3954
2.7483-2.9605	0.229	137	0.1741	3813	3950
2.9605-3.2584	0.1814	143	0.1619	3818	3961
3.2584-3.7297	0.1879	149	0.1497	3848	3997
3.7297-4.6985	0.1473	142	0.1277	3879	4021
4.6985-48.8674	0.1922	154	0.1549	4039	4193

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	3.4515	-0.8385	0.8849	3.8239	-0.8321	3.555	-0.0191	-0.0712	-0.2039	0.0554	-0.0314	-0.0809	0.3208	0.0984	0.0735	0.1428	0.0157	0.0015	0.1226	-0.0064	0.1094	-6.2123	-64.6195	-7.8808
2	2.7367	-0.8849	0.2096	2.4638	0.422	3.4788	-0.0355	0.2351	0.2042	-0.2192	-0.0957	-0.1846	-0.1079	0.2763	0.1024	0.1081	-0.0113	0.0022	0.1855	0.0392	0.1619	-5.7772	-52.9236	-12.5185
3	1.6988	-0.4541	-0.2728	2.8612	0.1588	1.8894	-0.0283	-0.1305	0.0236	0.1672	0.0522	-0.0826	0.139	0.0877	-0.0376	0.0979	0.0046	-0.009	0.1553	-0.0009	0.0787	-10.6158	-55.1251	0.6477
4	2.4236	-0.932	-0.0088	3.4407	-2.0428	5.246	0.1227	0.0855	-0.377	-0.1556	0.2151	0.4591	0.5368	-0.6126	-0.0687	0.1461	-0.0301	0.0174	0.1888	0.0044	0.2084	-24.3141	-58.0754	-3.4482
5	1.0195	-0.5806	-0.7584	1.9393	-0.0874	2.1065	0.0792	-0.1304	0.0584	0.1092	0.0914	0.1146	-0.1615	-0.0984	0.059	0.0925	-0.0093	0.0252	0.172	-0.018	0.1538	-20.1936	-47.4675	-1.0559
6	2.6335	0.5431	-1.229	3.196	-1.0324	4.3242	-0.1104	0.0737	0.2864	0.0365	0.0185	-0.2536	-0.6021	0.1324	0.056	0.2289	-0.0386	-0.0588	0.1574	-0.0031	0.1622	-9.4662	25.5335	-39.3146
7	2.2454	1.6487	-2.5796	3.0348	-1.1378	3.2609	-0.0696	-0.3971	0.2291	0.0727	0.0122	-0.0865	-0.0437	-0.1123	0.1224	0.1863	0.0359	-0.05	0.199	-0.0263	0.1496	-14.6137	15.4191	-29.0616
8	4.9337	3.0853	3.3095	4.0984	4.8776	5.8469	0.1594	0.0308	-0.0344	0.0111	0.2033	-0.6687	0.0893	0.6996	-0.4299	0.2004	0.0143	0.0196	0.2231	0.0022	0.2802	-3.6626	14.0995	-39.5668
9	3.1133	-0.4967	-0.8178	1.6605	1.7141	2.5699	-0.104	0.089	0.3054	-0.0128	0.0348	-0.2966	-0.3101	0.2751	0.0049	0.2351	-0.061	-0.048	0.155	0.025	0.1196	-10.8201	22.5724	-44.7685
10	2.1742	0.0348	0.0197	3.5507	0.1865	2.5263	-0.0682	0.0577	0.1211	-0.2198	0.1012	0.1415	-0.2682	-0.0838	-0.0322	0.1556	-0.0022	-0.0276	0.1335	0.0093	0.09	-20.3291	15.9951	-45.8723
11	1.8534	0.3777	0.7358	2.653	0.3116	3.5095	-0.0113	0.0448	0.0117	-0.1076	0.1374	0.1373	0.0321	-0.2028	-0.0271	0.1134	0.0137	-0.0162	0.1233	0.0075	0.1392	-24.5664	8.8824	-43.5618
12	0.8515	0.2639	-0.3068	0.6531	-0.027	5.0893	0.0572	-0.1665	-0.5791	-0.1451	-0.219	-0.2475	1.0335	0.3328	0.2728	0.4026	0.0399	0.0042	0.2157	0.1257	0.5795	-14.5119	-20.222	-36.8228
13	4.6523	-2.3271	2.28	2.9182	-1.3518	7.2535	0.1625	0.0889	-0.3469	-0.0966	-0.2112	-0.2976	0.4611	0.8334	0.0696	0.1808	-0.0132	-0.0132	0.2116	0.0628	0.3499	-10.1378	-10.6454	-39.5273
14	0.8177	-0.5182	-0.3336	9.118	1.3611	2.6272	0.045	-0.3213	-0.4045	0.4354	0.0444	-0.3177	0.3143	0.0072	-0.0821	0.1516	-0.0136	-0.0487	0.2176	0.1066	0.3068	-17.9257	-7.7069	-30.7385
15	1.8784	0.6432	-0.0176	3.2745	-0.5926	2.6457	0.077	-0.1464	-0.6995	0.0467	0.0797	0.1157	0.3601	-0.2556	-0.0732	0.2083	-0.0673	-0.0413	0.213	0.0848	0.3854	-26.7666	-11.5589	-35.4611
16	2.8688	-0.1877	-1.6897	1.9353	-0.328	4.9351	0.0005	0.0817	-0.1963	-0.2005	0.1404	0.3813	0.1683	-0.3053	-0.083	0.1703	-0.0547	-0.038	0.1682	0.0047	0.2177	-27.43	-2.7862	-45.3924
17	5.8311	-1.1352	-2.8861	7.6391	0.778	4.9401	-0.1118	-0.2291	0.338	1.165	0.3805	0.2527	-0.1429	-0.0749	-0.2804	0.4059	0.0254	0.1299	0.422	0.0563	0.217	-26.8688	2.7001	-20.8821
18	1.278	-1.0246	0.1622	0.8305	-0.063	4.2968	0.2111	0.1395	0.6868	-0.0325	-0.1623	-0.0955	-0.9666	0.1911	-0.0214	0.6912	-0.0493	-0.0185	0.2018	0.0401	0.5489	-12.0726	-18.2219	-9.6484
19	1.9199	1.3881	-0.7833	3.6015	-1.6606	8.0854	0.6265	-0.4604	0.772	0.5706	-0.5058	0.3182	-1.0781	0.5248	-0.2016	0.3248	-0.0575	0.0059	0.1929	-0.0269	0.2914	-9.2835	-28.2877	0.9909
20	4.7632	1.7341	0.5618	4.1925	-0.1438	8.6337	0.1018	0.1851	0.4787	-0.0508	0.0141	0.0304	-0.8802	0.7834	-0.0674	0.344	-0.031	0.0552	0.2556	0.067	0.282	-5.7056	-27.5871	-13.6624
21	1.1287	0.3143	-0.1244	4.9644	0.3613	0.0571	-0.0278	0.1191	0.6669	-0.313	-0.045	0.1186	-0.9015	-0.0962	-0.0836	0.6266	0.0872	-0.0276	0.1878	0.072	0.4001	-16.2881	-21.8542	-13.8021
22	1.8292	0.7864	0.2247	4.2236	0.4912	1.0636	-0.1148	0.0624	0.3698	-0.0151	0.1549	0.2033	-0.6464	-0.1313	-0.0408	0.3171	0.0774	-0.0186	0.2037	0.0266	0.2581	-18.802	-32.7045	-10.8206
23	1.2589	-0.2597	-0.2127	2.5503	0.1119	0.3474	0.08	0.2745	0.5495	-0.392	-0.0191	0.3506	-0.6334	-0.4925	0.0386	0.3805	0.147	-0.0399	0.3081	0.0543	0.35	-24.7816	-29.2445	-15.2068
24	3.5817	-0.1966	0.8887	3.47	0.0851	1.8096	0.0257	-0.4162	0.6285	0.2596	-0.0925	0.4891	-0.5926	-0.7013	-0.0781	0.411	0.1696	0.0492	0.3198	-0.108	0.4619	-27.1264	-28.3803	-0.0237
25	0.8173	0.6858	0.0014	2.1906	0.488	0.6915	0.0261	-0.2913	0.3273	0.2297	-0.0425	0.3232	-0.435	-0.4909	0.0592	0.2175	0.0741	0.0308	0.2392	-0.054	0.2378	-22.5395	-36.1952	1.7871
26	3.1562	0.947	0.5233	3.1165	0.455	1.5168	-0.2356	0.6512	0.0158	-0.7448	0.4125	0.3863	-0.2562	-0.2838	-0.0279	0.3857	0.0007	-0.1138	0.4103	0.0812	0.2895	-26.236	-41.1611	-23.0237

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 25 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 50 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 121 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 122 through 137 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 179 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 0 through 25 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 26 through 36 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 37 through 50 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 51 through 71 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 72 through 137 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 138 through 179 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 25 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 26 through 50 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 51 through 80 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 81 through 136 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 137 through 164 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 165 through 178 )	C
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1 through 25 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 26 through 36 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 37 through 50 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 51 through 71 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 72 through 96 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 97 through 121 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 122 through 137 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 138 through 164 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 165 through 179 )	D

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