PDB-6wng: Crystal structure of an aspartate ammonia-lyase from Elizabethkin...

ID or keywords:

Entry

Database: PDB / ID: 6wng

Title

Crystal structure of an aspartate ammonia-lyase from Elizabethkingia anophelis NUHP1

Components

Aspartate ammonia-lyase

Keywords

LYASE / NIAID / National Institute of Allergy and Infectious Disease / emergent pathogen / bacterium / flavobacteriales / asparate / fumarate / alanine and asparate metabolism / nitrogen metabolism / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

aspartate ammonia-lyase / aspartate ammonia-lyase activity / aspartate metabolic process / tricarboxylic acid cycle
Similarity search - Function

Biological species

Elizabethkingia anophelis NUH1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of an aspartate ammonia-lyase from Elizabethkingia anophelis NUHP1
Authors: Edwards, T.E. / Mayclin, S.J. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease

History

Deposition	Apr 22, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wng.cif.gz	759.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6wng.ent.gz	625.6 KB	Display	PDB format
PDBx/mmJSON format	6wng.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wn/6wng ftp://data.pdbj.org/pub/pdb/validation_reports/wn/6wng	HTTPS FTP

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Related structure data

Related structure data	3oceS S: Starting model for refinement
Similar structure data	2ptq-1 7c1c-d 7c1a-d 7c18-d 3gzh-1 7miw-d 5nxa-2 2ynm-d 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: ElanA.00047.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (9) #127 - Jul 2010 Crystallins similarity (7)

Deposited unit

A: Aspartate ammonia-lyase

B: Aspartate ammonia-lyase

C: Aspartate ammonia-lyase

D: Aspartate ammonia-lyase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	92.820, 96.850, 212.200
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Aspartate ammonia-lyase / Aspartase Mass: 52529.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia anophelis NUH1 (bacteria) Strain: NUHP1 / Gene: BD94_1127 / Production host: Escherichia coli (E. coli) References: UniProt: X5KSV5, UniProt: A0A077EBQ3*PLUS, aspartate ammonia-lyase

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Non-polymers , 5 types, 2131 molecules

#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Chemical	ChemComp-FUM / FUMARIC ACID Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2107 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.27 Å³/Da / Density % sol: 45.87 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ElanA.00047.a.B1.PW38143 at 13.07 mg/mL with 2.5 mM aspartic acid against JCSG+ screen condition D1 25% PEG 1500, 20% glycerol, unique puck ID aue0-7, crystal tracking ID 314597d1

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 20, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.55→46.06 Å / Num. obs: 275981 / % possible obs: 99.9 % / Redundancy: 6.043 % / B_iso Wilson estimate: 21.591 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.077 / R_rim(I) all: 0.085 / Χ²: 1.072 / Net I/σ(I): 14.36 / Num. measured all: 1667799 / Scaling rejects: 5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.55-1.59	5.988	0.499	3.53	121252	20251	20249	0.89	0.548	100
1.59-1.63	6.191	0.428	4.22	122395	19769	19769	0.915	0.469	100
1.63-1.68	6.203	0.356	5.03	119258	19226	19225	0.943	0.389	100
1.68-1.73	6.205	0.298	6.02	115693	18646	18645	0.954	0.325	100
1.73-1.79	6.221	0.241	7.34	112841	18139	18140	0.969	0.263	100
1.79-1.85	6.199	0.196	8.84	108547	17509	17509	0.979	0.215	100
1.85-1.92	6.094	0.164	10.81	103002	16909	16902	0.983	0.179	100
1.92-2	6.136	0.136	12.58	100003	16303	16298	0.988	0.148	100
2-2.09	6.008	0.113	14.78	93985	15647	15643	0.991	0.124	100
2.09-2.19	6.038	0.092	17.31	90539	14999	14994	0.993	0.101	100
2.19-2.31	5.842	0.082	19.26	83300	14276	14260	0.994	0.09	99.9
2.31-2.45	5.911	0.074	20.94	79545	13467	13456	0.995	0.081	99.9
2.45-2.62	5.861	0.069	22.32	74649	12741	12736	0.995	0.075	100
2.62-2.83	5.819	0.064	23.56	68923	11852	11844	0.996	0.07	99.9
2.83-3.1	5.832	0.058	25.37	63885	10962	10955	0.997	0.063	99.9
3.1-3.47	5.822	0.053	27.16	57738	9937	9917	0.997	0.059	99.8
3.47-4	5.925	0.047	29.34	51968	8788	8771	0.998	0.052	99.8
4-4.9	6.055	0.041	30.64	45353	7507	7490	0.998	0.045	99.8
4.9-6.93	6.096	0.039	30.24	35684	5880	5854	0.998	0.042	99.6
6.93-46.06	5.788	0.033	30.79	19239	3389	3324	0.998	0.036	98.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3oce

3oce

Resolution: 1.55→46.06 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.36

	R_factor	Num. reflection	% reflection
R_free	0.1527	2053	0.74 %
R_work	0.1339	-	-
obs	0.134	275964	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 75.2 Å² / B_iso mean: 18.4133 Å² / B_iso min: 5.8 Å²

Refinement step

Cycle: final / Resolution: 1.55→46.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14306	0	106	2118	16530
B_iso mean	-	-	24.44	30.85	-
Num. residues	-	-	-	-	1864

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.59	0.1857	159	0.1665	18098	18257	100
1.59-1.63	0.2069	118	0.1603	18069	18187	100
1.63-1.67	0.2008	132	0.1564	18148	18280	100
1.67-1.72	0.1662	127	0.1591	18193	18320	100
1.72-1.77	0.1603	127	0.1471	18112	18239	100
1.77-1.84	0.1804	149	0.1426	18164	18313	100
1.84-1.91	0.143	136	0.1371	18161	18297	100
1.91-2	0.1783	155	0.1417	18153	18308	100
2-2.1	0.1686	164	0.1404	18198	18362	100
2.1-2.24	0.1477	150	0.1275	18224	18374	100
2.24-2.41	0.1352	124	0.1267	18255	18379	100
2.41-2.65	0.1611	150	0.1301	18328	18478	100
2.65-3.03	0.1159	95	0.1296	18391	18486	100
3.03-3.82	0.1386	122	0.1224	18501	18623	100
3.82-46.06	0.1423	145	0.1277	18916	19061	99

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	1.0094	-0.1501	-0.013	0.9031	-0.1055	0.6455	-0.0093	-0.1975	0.031	0.186	-0.0015	-0.0505	-0.0364	0.0446	0.0104	0.116	-0.0034	-0.0057	0.1242	-0.0104	0.0648	-2.9476	12.175	57.7983
2	0.3118	0.1719	0.0198	0.3466	-0.0051	0.1713	-0.0088	-0.0325	-0.0532	0.0052	0.0011	-0.02	0.0448	-0.017	0.0018	0.1005	0.0091	0.0132	0.0971	0.0057	0.0939	-16.6684	-10.7688	38.2911
3	0.5035	0.0595	-0.0671	0.2752	-0.0436	0.5955	0.0079	0.0505	-0.1974	0.0026	-0.0165	0.0814	0.2788	-0.1343	-0.0091	0.1636	-0.0096	-0.0119	0.117	-0.0122	0.1841	-30.1845	-27.4912	26.1936
4	1.5067	0.1012	-0.4312	1.2589	0.401	1.1984	-0.0224	-0.2135	-0.0708	0.3295	-0.0127	0.1288	0.1198	-0.0998	0.0481	0.1817	0.0085	0.0283	0.1822	0.0134	0.11	-39.7293	-5.8454	56.8698
5	2.7709	0.5491	0.8107	0.949	0.2136	0.978	-0.0483	-0.1682	0.184	0.0996	-0.0013	0.2649	-0.0199	-0.1768	0.029	0.1274	0.0304	0.0573	0.1665	-0.0083	0.2116	-55.2868	8.5475	49.657
6	1.4233	0.0404	-0.0672	0.9653	0.0287	0.9994	-0.0166	-0.3056	-0.0188	0.2392	-0.0043	0.2512	-0.0093	-0.1933	0.0078	0.1399	0.0159	0.0669	0.1982	-0.005	0.1772	-48.9277	0.1707	54.0758
7	2.5242	2.6174	-0.5646	3.1188	-0.6062	0.3123	0.0338	-0.0853	0.2307	0.0272	-0.0132	0.2954	-0.0451	-0.0539	-0.0321	0.0868	0.029	0.0049	0.1175	-0.008	0.1341	-34.1873	20.4947	37.1977
8	0.6671	0.4317	-0.3692	0.5192	-0.2292	0.3061	0.0034	-0.0113	0.1154	-0.0162	0.0295	0.1367	-0.0476	-0.0556	-0.0312	0.1176	0.0196	-0.0131	0.108	0.0059	0.1305	-22.1203	27.8038	25.3347
9	0.6886	0.3439	-0.0762	0.8673	0.0888	0.4051	-0.0045	0.0202	0.1243	-0.0272	-0.0036	0.2167	-0.0458	-0.0958	0.0009	0.1032	0.0132	0.0025	0.1837	0.0129	0.237	-54.4477	5.5423	34.4186
10	0.3575	0.3086	0.0767	0.4255	0.0843	0.176	-0.0027	-0.0392	0.0331	0.015	-0.0022	0.0596	-0.0177	-0.0392	0.0073	0.0822	0.0158	0.0061	0.1046	-0.0007	0.1008	-20.3274	15.0462	35.6002
11	0.3495	0.1759	-0.3126	0.4358	-0.3059	1.6052	-0.0089	0.0113	0.0443	-0.0901	-0.0086	-0.0197	-0.1348	0.1589	0.0217	0.1577	-0.008	0.0035	0.0975	0.0047	0.1284	-3.4744	36.6167	15.1802
12	2.264	-0.4604	-0.1874	1.6145	-0.3395	1.2449	0.1091	0.0542	0.2096	-0.1335	-0.0278	-0.1077	-0.1327	0.1029	-0.0988	0.2198	-0.0103	-0.0006	0.1136	-0.0047	0.1666	-4.9793	45.801	8.8261
13	1.2401	0.0782	-0.2532	1.1655	0.5148	1.2953	-0.0142	0.281	-0.0804	-0.2814	-0.0403	0.0688	0.0757	-0.1587	0.067	0.2336	-0.0223	-0.0223	0.1968	-0.0027	0.0999	-28.3913	-17.7086	-2.7125
14	0.7991	-0.0127	-0.1515	2.3877	-0.8273	1.2132	0.0067	0.0316	-0.087	-0.2091	-0.051	-0.2009	0.1589	0.1067	0.0229	0.183	-0.0022	0.0444	0.1363	-0.0187	0.1302	-11.5652	-30.758	4.5759
15	0.5858	0.1016	0.0799	1.2243	0.4012	0.5562	-0.008	0.1922	-0.1297	-0.2302	-0.0203	-0.0436	0.1004	0.0185	0.0018	0.2138	-0.0122	0.0219	0.1629	-0.0288	0.1384	-20.9605	-25.8441	0.27
16	1.0993	1.1948	0.3068	1.7303	0.4755	0.2829	-0.0666	0.0155	-0.1803	-0.1687	0.0675	-0.2228	0.0177	0.0447	-0.0484	0.1176	0.0102	0.0347	0.0951	-0.0008	0.1244	-2.0191	-7.683	16.0244
17	0.23	0.2461	0.0197	0.7725	0.1379	0.173	-0.0156	-0.003	-0.0767	-0.0527	0.0112	-0.1035	0.0501	0.0138	-0.0025	0.1117	0.0116	0.016	0.1136	0.0018	0.1134	-5.3704	-8.2006	23.6876
18	0.6421	0.1114	0.2388	0.7145	-0.2133	0.7377	-0.0393	0.0583	0.0292	-0.1184	0.0241	-0.0154	-0.0277	0.0304	0.0074	0.123	-0.0074	0.0214	0.0933	0.0053	0.0977	-1.0669	24.1771	12.8298
19	0.7435	0.7598	-0.2057	1.0851	-0.2453	0.2141	-0.0728	0.0155	-0.0552	-0.1395	0.032	-0.0422	0.0435	-0.0089	0.0274	0.105	0.0038	0.0083	0.0845	-0.0041	0.0807	-14.586	-2.4252	16.6305
20	0.3888	0.4032	0.5891	0.8867	0.9088	2.1782	-0.011	-0.0085	0.0321	-0.0385	0.0396	-0.1028	-0.2207	0.0928	-0.0491	0.0874	-0.0028	0.0039	0.1133	-0.0128	0.1534	10.2183	25.0192	36.4301
21	1.1058	0.6091	0.1626	2.8683	1.3398	1.664	0.0299	-0.0089	0.0613	-0.0078	0.1174	-0.3151	-0.1867	0.252	-0.1641	0.1239	-0.0243	-0.0075	0.1834	-0.0239	0.2194	19.572	24.5984	43.2628
22	0.5344	0.2136	0.1745	0.4194	-0.3883	1.2548	-0.1284	0.2346	-0.0498	-0.3723	0.0971	-0.0912	0.0273	0.13	0.0318	0.244	-0.0385	0.0464	0.1565	-0.022	0.1059	-7.6478	14.304	-4.4797
23	0.6021	-0.0435	0.1641	0.6985	-0.1104	0.5857	-0.1093	0.1965	0.0801	-0.3785	0.0727	0.0631	-0.0447	-0.0598	0.0167	0.2554	-0.0446	-0.0436	0.157	0.0284	0.106	-19.2756	25.0303	-5.4149
24	1.772	1.9752	-0.6625	2.7276	-0.7966	0.5161	-0.0965	0.0663	0.1908	-0.1768	0.1162	0.2985	0.0142	-0.1401	-0.0256	0.1138	0.0065	-0.0398	0.1256	0.0137	0.105	-37.1938	9.0637	9.2793
25	0.2555	0.1747	-0.0005	0.4241	-0.0181	0.1533	-0.0399	0.0222	0.0413	-0.0936	0.0373	0.1148	0.0102	-0.0666	-0.0077	0.1015	0.0003	-0.0201	0.1294	0.0037	0.113	-35.2822	4.2575	17.0245
26	3.0931	3.3003	0.7614	3.509	0.9495	0.2769	-0.159	0.0975	-0.0079	-0.2331	0.1347	0.0326	-0.0603	-0.0471	0.0328	0.1286	-0.0011	-0.0133	0.1109	0.0163	0.0938	-26.0666	6.8279	11.5974
27	0.8774	0.2591	-0.8925	0.5694	-0.3985	2.0958	-0.0432	-0.0261	-0.0667	0.0398	0.0714	0.1948	0.1948	-0.2217	-0.0189	0.1299	-0.0378	0.0144	0.2048	0.0285	0.2514	-55.5381	-17.8226	34.2945
28	1.0852	0.6381	-0.7751	0.9351	-0.8757	1.0471	0.0148	0.0644	-0.1506	0.0314	0.3046	0.6815	0.0848	-0.4534	-0.2246	0.2117	-0.0558	0.063	0.3674	0.0679	0.5119	-66.4227	-16.448	38.0612

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 149 )	A	10 - 149
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 362 )	A	150 - 362
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 363 through 475 )	A	363 - 475
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 10 through 51 )	B	10 - 51
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 52 through 91 )	B	52 - 91
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 92 through 149 )	B	92 - 149
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 150 through 186 )	B	150 - 186
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 187 through 232 )	B	187 - 232
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 233 through 280 )	B	233 - 280
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 281 through 395 )	B	281 - 395
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 396 through 440 )	B	396 - 440
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 441 through 475 )	B	441 - 475
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 10 through 51 )	C	10 - 51
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 52 through 91 )	C	52 - 91
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 92 through 149 )	C	92 - 149
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 150 through 186 )	C	150 - 186
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 187 through 307 )	C	187 - 307
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 308 through 336 )	C	308 - 336
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 337 through 395 )	C	337 - 395
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 396 through 440 )	C	396 - 440
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 441 through 475 )	C	441 - 475
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 10 through 51 )	D	10 - 51
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 52 through 149 )	D	52 - 149
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 150 through 186 )	D	150 - 186
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 187 through 362 )	D	187 - 362
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 363 through 395 )	D	363 - 395
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 396 through 440 )	D	396 - 440
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 441 through 475 )	D	441 - 475

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