PDB-8wwu: 1-naphthylamine GS in complex with AMP PNP

ID or keywords:

Entry

Database: PDB / ID: 8wwu

Title

1-naphthylamine GS in complex with AMP PNP

Components

Glutamine synthetase

Keywords

LIGASE /

glutamine synthetase / 1-naphthylamine glutamine synthetase

Function / homology

Function and homology information

glutamine biosynthetic process /

glutamine synthetase activity
Similarity search - Function

Biological species

Pseudomonas lactis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Zhang, S.T. / Zhou, N.Y.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Discovery of the 1-naphthylamine biodegradation pathway reveals a glutamine synthetase-like protein that catalyzes 1-naphthylamine glutamylation
Authors: Zhang, S.T. / Zhou, N.Y.

History

Deposition	Oct 26, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wwu.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8wwu.ent.gz		Display	PDB format
PDBx/mmJSON format	8wwu.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/ww/8wwu ftp://data.pdbj.org/pub/pdb/validation_reports/ww/8wwu	HTTPS FTP

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Related structure data

Related structure data	8wwvC C: citing same article (ref.)
Similar structure data	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	#30 - Jun 2002 Glutamine Synthetase similarity (7) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#30 - Jun 2002
Glutamine Synthetase
similarity (7)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

F: Glutamine synthetase

hetero molecules

345 kDa, 6 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)	123.685, 140.567, 217.028
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glutamine synthetase / Mass: 56933.402 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas lactis (bacteria) / Gene: HBO18_29070 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y1Q2L1
#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2109 / 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: 2.89 Å³/Da / Density % sol: 57.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M magnesium chloride hexahydrate, 0.1 M rubidium chloride, 0.1 M PIPES 7.0 and 20 % v/v PEG smear low

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2→49.69 Å / Num. obs: 251047 / % possible obs: 98.6 % / Redundancy: 7.3 % / CC_1/2: 0.996 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2→2.03 Å / Num. unique obs: 11527 / CC_1/2: 0.891

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: 000)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→43.817 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2065	12575	5.02 %
R_work	0.1795	-	-
obs	0.1809	250611	98.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→43.817 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22991	0	204	2109	25304

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	23813
X-RAY DIFFRACTION	f_angle_d	1.099	32361
X-RAY DIFFRACTION	f_dihedral_angle_d	8.292	14200
X-RAY DIFFRACTION	f_chiral_restr	0.065	3512
X-RAY DIFFRACTION	f_plane_restr	0.007	4174

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 (%)
2-2.0207	0.3619	411	0.2931	7199	X-RAY DIFFRACTION	90
2.0207-2.0445	0.3178	433	0.2683	7575	X-RAY DIFFRACTION	95
2.0445-2.0694	0.2905	403	0.2482	7754	X-RAY DIFFRACTION	97
2.0694-2.0956	0.2754	396	0.2366	7952	X-RAY DIFFRACTION	99
2.0956-2.1232	0.2669	442	0.2218	7976	X-RAY DIFFRACTION	100
2.1232-2.1523	0.2679	437	0.219	7958	X-RAY DIFFRACTION	100
2.1523-2.183	0.2472	425	0.2104	7946	X-RAY DIFFRACTION	100
2.183-2.2156	0.2389	429	0.2056	7985	X-RAY DIFFRACTION	100
2.2156-2.2502	0.2354	438	0.197	8011	X-RAY DIFFRACTION	100
2.2502-2.2871	0.2385	414	0.1947	7973	X-RAY DIFFRACTION	100
2.2871-2.3265	0.2162	408	0.1885	8004	X-RAY DIFFRACTION	100
2.3265-2.3688	0.235	389	0.187	8056	X-RAY DIFFRACTION	100
2.3688-2.4144	0.2203	431	0.1883	7861	X-RAY DIFFRACTION	98
2.4144-2.4637	0.2125	429	0.179	7831	X-RAY DIFFRACTION	98
2.4637-2.5172	0.2054	427	0.1801	7990	X-RAY DIFFRACTION	100
2.5172-2.5758	0.2169	417	0.1858	7993	X-RAY DIFFRACTION	99
2.5758-2.6402	0.2329	398	0.1887	8015	X-RAY DIFFRACTION	99
2.6402-2.7116	0.2283	401	0.191	8048	X-RAY DIFFRACTION	99
2.7116-2.7913	0.2506	418	0.1964	7997	X-RAY DIFFRACTION	99
2.7913-2.8814	0.2241	449	0.1892	7961	X-RAY DIFFRACTION	99
2.8814-2.9844	0.2346	443	0.1915	7979	X-RAY DIFFRACTION	99
2.9844-3.1039	0.2111	390	0.1851	7830	X-RAY DIFFRACTION	97
3.1039-3.2451	0.1927	413	0.1844	8035	X-RAY DIFFRACTION	99
3.2451-3.4161	0.1919	443	0.1816	8020	X-RAY DIFFRACTION	99
3.4161-3.63	0.1902	407	0.1655	8009	X-RAY DIFFRACTION	99
3.63-3.9101	0.1714	396	0.1539	8049	X-RAY DIFFRACTION	99
3.9101-4.3033	0.1417	421	0.1368	7879	X-RAY DIFFRACTION	97
4.3033-4.9253	0.1503	391	0.1308	8083	X-RAY DIFFRACTION	98
4.9253-6.2026	0.1673	428	0.1542	8056	X-RAY DIFFRACTION	97
6.2026-43.817	0.1767	448	0.1678	8011	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	1.3498	-0.0622	0.2117	1.0432	0.324	0.9088	-0.0119	-0.2477	-0.2207	0.2199	0.0331	-0.1125	0.3048	0.1812	0.0057	0.3026	0.0632	-0.037	0.2528	0.032	0.2249	-11.692	-5.492	19.426
2	0.4355	0.122	-0.2085	0.6964	-0.021	1.0652	-0.0158	0.0104	-0.0513	0.0032	0.0068	-0.0114	0.127	0.0335	-0.0113	0.2058	-0.0062	-0.0312	0.176	-0.0075	0.2072	-19.517	-0.199	-0.871
3	1.1288	-0.0632	-0.2064	1.4143	-0.0368	1.0439	-0.014	0.1634	-0.2417	-0.1819	-0.0403	0.135	0.3879	-0.0374	-0.0003	0.325	-0.0223	-0.0398	0.1813	-0.0355	0.2402	-24.582	-17.84	-3.71
4	1.1469	0.0146	-0.2421	1.0595	0.2035	1.0502	-0.0163	0.2285	0.2268	-0.2848	0.0289	-0.1404	-0.3538	0.2046	0.0287	0.3231	-0.081	-0.0059	0.2754	0.0183	0.2657	-11.028	75.716	-15.381
5	0.4735	-0.0232	0.1167	0.7232	-0.0299	1.0444	-0.0189	0.0044	0.0533	-0.0163	0.0011	-0.0135	-0.1312	0.0316	0.0085	0.2004	0.0063	-0.0097	0.1826	-0.0055	0.2178	-19.668	70.431	4.578
6	0.9151	0.2367	0.2443	1.4046	0.1512	1.2246	-0.0665	-0.1572	0.2344	0.1086	-0.0217	0.0918	-0.4295	-0.108	0.0222	0.375	0.0511	-0.0353	0.2158	-0.0334	0.2921	-24.88	88.085	7.219
7	0.8181	-0.0889	-0.4842	0.8058	-0.2851	2.5887	0.1061	-0.2811	-0.0577	0.4145	-0.0299	-0.4977	0.1469	0.4299	-0.0004	0.4311	-0.0032	-0.199	0.4065	-0.0277	0.4313	1.752	29.031	46.022
8	0.4114	0.0008	0.039	1.0827	0.0273	0.5289	-0.0097	-0.0961	0.0584	0.4014	0.0181	-0.0912	-0.0004	0.0653	-0.0008	0.3302	0.0076	-0.0607	0.222	0.0016	0.1865	-15.428	25.424	44.559
9	0.1487	-0.053	-0.0917	0.8919	0.1513	0.7971	-0.0007	0.0398	0.0226	0.057	-0.0072	-0.0183	0.0815	0.0064	-0.0066	0.2092	-0.0152	-0.0318	0.2051	0.0158	0.1761	-21.572	15.353	25.723
10	0.8742	-0.2702	0.2876	0.8903	-0.2605	0.8664	-0.092	0.0078	-0.1434	0.2429	0.1083	-0.2263	0.1325	0.1353	-0.0029	0.4245	0.0334	-0.1107	0.2451	0.0079	0.2709	-8.655	-3.611	44.152
11	0.8276	-0.2709	-0.0888	0.8931	-0.1223	0.6113	-0.0294	-0.0225	-0.1984	0.3544	0.0137	0.1328	0.3442	-0.0297	-0.0199	0.3875	-0.0168	-0.0105	0.2113	0.0199	0.2003	-23.693	-0.926	43.831
12	0.667	-0.0651	0.0226	1.206	-0.111	1.2368	-0.0389	-0.0942	-0.0554	0.4488	0.0617	0.2448	0.034	-0.181	-0.0305	0.4082	-0.0185	0.0762	0.239	0.0243	0.2564	-33.683	15.367	46.253
13	0.7437	-0.2475	0.1066	1.0908	-0.0649	0.9033	0.0226	0.2267	-0.0684	-0.3929	-0.0316	-0.2688	-0.036	0.2364	0.0022	0.3183	-0.0003	0.0811	0.3072	-0.0011	0.2918	-8.134	39.571	-40.309
14	0.6721	0.256	-0.1616	1.0861	0.138	0.7906	-0.0353	0.1846	-0.0317	-0.452	0.0328	-0.0604	0.1717	0.0626	0.0271	0.3779	-0.0036	0.0531	0.2689	0.0024	0.2609	-12.84	41.099	-42.753
15	0.2856	0.0567	0.1508	1.0685	0.1444	0.8583	-0.0098	0.0212	0.0122	-0.1019	0.0013	-0.0572	-0.0552	0.063	0.0059	0.2132	0.0005	0.0058	0.2196	0.0171	0.1951	-18.694	55.256	-27.108
16	1.0954	0.5532	0.0982	1.265	-0.1265	1.2096	-0.0834	0.103	0.2628	-0.2185	0.0192	-0.2528	-0.3009	0.4262	0.0187	0.4909	-0.0769	0.0607	0.3646	0.0555	0.3718	-8.415	75.045	-42.511
17	0.8388	0.149	0.2294	0.9467	-0.13	0.7769	-0.0267	0.0197	0.2813	-0.2746	-0.0123	0.0635	-0.4486	-0.0073	0.0014	0.4352	-0.0047	-0.0135	0.2575	0.0235	0.2755	-22.69	70.716	-39.641
18	0.6251	0.1572	-0.0083	1.2139	-0.0846	1.2848	0.0575	0.0903	0.1129	-0.3756	0.0212	0.2037	-0.1262	-0.1318	-0.019	0.3583	0.021	-0.0777	0.2455	0.0254	0.2576	-31.966	54.969	-43.082
19	0.9946	0.0328	0.1702	1.0282	-0.0707	0.9513	0.0579	0.1451	-0.1791	-0.2317	-0.0625	-0.2955	0.2943	0.3516	-0.0229	0.308	0.0886	0.0476	0.3353	-0.0162	0.3019	-4.014	1.032	-22.514
20	2.165	-0.1165	0.1372	0.7226	-0.2466	0.4666	-0.0743	0.1238	-0.563	-0.4172	0.0745	0.0089	0.5927	0.0185	-0.0268	0.5424	0.0044	0.0086	0.2929	-0.0443	0.301	-21.753	-5.797	-27.678
21	0.5112	0.2264	0.0272	1.0677	-0.1838	0.7341	0.0059	0.0542	-0.0348	-0.1828	0.0051	-0.0749	0.0733	0.0501	-0.004	0.231	0.0115	-0.0056	0.2269	-0.0188	0.1785	-17.501	18.627	-29.005
22	0.7727	0.1882	0.0345	1.2762	-0.0901	1.1047	-0.0216	0.1858	-0.0167	-0.4913	0.0725	-0.016	0.1316	-0.0204	-0.0096	0.4502	-0.0225	-0.0364	0.2461	-0.0246	0.1793	-23.545	14.005	-46.578
23	1.1345	0.1148	-0.1481	0.9291	-0.1612	1.0414	0.0493	-0.0414	0.2911	0.1502	-0.0423	-0.1919	-0.3396	0.1466	-0.0121	0.2761	-0.0483	-0.0473	0.2153	-0.0123	0.2585	-11.961	70.007	28.22
24	0.5032	-0.1654	0.0353	1.1859	-0.0639	0.9457	-0.0093	-0.0919	0.0347	0.3256	0.0148	-0.0086	-0.0281	-0.0264	0.0022	0.2424	-0.0048	-0.0082	0.1813	-0.0212	0.1549	-23.02	53.579	42.798

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 4:129 )	A	4 - 129
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 130:289 )	A	130 - 289
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 290:495 )	A	290 - 495
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 4:129 )	B	4 - 129
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 130:289 )	B	130 - 289
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 290:495 )	B	290 - 495
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 5:32 )	C	5 - 32
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 33:172 )	C	33 - 172
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 173:289 )	C	173 - 289
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 290:315 )	C	290 - 315
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 316:430 )	C	316 - 430
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 431:495 )	C	431 - 495
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 4:84 )	D	4 - 84
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 85:129 )	D	85 - 129
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 130:291 )	D	130 - 291
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 292:327 )	D	292 - 327
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 328:430 )	D	328 - 430
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 431:495 )	D	431 - 495
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 6:64 )	E	6 - 64
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 65:110 )	E	65 - 110
21	X-RAY DIFFRACTION	21	( CHAIN E AND RESID 111:291 )	E	111 - 291
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 292:495 )	E	292 - 495
23	X-RAY DIFFRACTION	23	( CHAIN F AND RESID 6:129 )	F	6 - 129
24	X-RAY DIFFRACTION	24	( CHAIN F AND RESID 130:495 )	F	130 - 495

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi