PDB-8wwv: 1-naphthylamine GS in complex with ADP and MetSox-P

ID or keywords:

Entry

Database: PDB / ID: 8wwv

Title

1-naphthylamine GS in complex with ADP and MetSox-P

Components

Glutamine synthetase

Keywords

LIGASE / glutamine synthetase / 1-naphthylamine glutamine synthetase

Function / homology

Function and homology information

glutamine biosynthetic process / glutamine synthetase activity / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Pseudomonas lactis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

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

Funding support

China, 2items

Citation

Journal: Elife / Year: 2024
Title: Discovery of the 1-naphthylamine biodegradation pathway reveals a broad-substrate-spectrum enzyme catalyzing 1-naphthylamine glutamylation.
Authors: Zhang, S.T. / Deng, S.K. / Li, T. / Maloney, M.E. / Li, D.F. / Spain, J.C. / 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
Revision 1.1	Jan 15, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wwv.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb8wwv.ent.gz		Display	PDB format
PDBx/mmJSON format	8wwv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wwv_validation.pdf.gz	10.2 MB	Display	wwPDB validaton report
Full document	8wwv_full_validation.pdf.gz	10.2 MB	Display
Data in XML	8wwv_validation.xml.gz	104.8 KB	Display
Data in CIF	8wwv_validation.cif.gz	144.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ww/8wwv ftp://data.pdbj.org/pub/pdb/validation_reports/ww/8wwv	HTTPS FTP

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Related structure data

Related structure data	8wwuC 8x6zC 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)

Deposited unit

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

F: Glutamine synthetase

hetero molecules

347 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	123.058, 140.482, 216.657
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 5 types, 687 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE Mass: 260.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₁₃N₂O₆PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.62 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 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 / 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: 2.3→46.84 Å / Num. obs: 166648 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.153 / R_pim(I) all: 0.043 / R_rim(I) all: 0.159 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.3→2.34 Å / R_merge(I) obs: 1.286 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8158 / CC_1/2: 0.905 / R_pim(I) all: 0.356 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: 000)	refinement
XDS		data reduction
Aimless	CCP4Interface 7.0.065	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→43.77 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2317	8302	4.99 %
R_work	0.2119	-	-
obs	0.2129	166648	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→43.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22951	0	270	657	23878

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	23771
X-RAY DIFFRACTION	f_angle_d	1.054	32311
X-RAY DIFFRACTION	f_dihedral_angle_d	15.9	8711
X-RAY DIFFRACTION	f_chiral_restr	0.055	3502
X-RAY DIFFRACTION	f_plane_restr	0.008	4164

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 (%)
2.3-2.33	0.3414	524	0.327	10203	X-RAY DIFFRACTION	100
2.33-2.35	0.3202	525	0.3111	10125	X-RAY DIFFRACTION	100
2.35-2.38	0.3436	547	0.3067	10222	X-RAY DIFFRACTION	100
2.38-2.41	0.343	507	0.2991	10228	X-RAY DIFFRACTION	100
2.41-2.44	0.3365	489	0.293	10219	X-RAY DIFFRACTION	100
2.44-2.48	0.2883	589	0.2772	10095	X-RAY DIFFRACTION	100
2.48-2.51	0.2929	542	0.2766	10226	X-RAY DIFFRACTION	100
2.51-2.55	0.2883	575	0.2773	10208	X-RAY DIFFRACTION	100
2.55-2.59	0.2602	514	0.2779	10169	X-RAY DIFFRACTION	100
2.59-2.63	0.3017	533	0.2675	10171	X-RAY DIFFRACTION	100
2.63-2.68	0.2541	549	0.2716	10208	X-RAY DIFFRACTION	100
2.68-2.73	0.2915	552	0.2615	10129	X-RAY DIFFRACTION	100
2.73-2.78	0.2773	563	0.2631	10195	X-RAY DIFFRACTION	100
2.78-2.84	0.2946	516	0.2688	10172	X-RAY DIFFRACTION	100
2.84-2.9	0.2755	493	0.2554	10218	X-RAY DIFFRACTION	100
2.9-2.97	0.2778	480	0.2479	10275	X-RAY DIFFRACTION	100
2.97-3.04	0.272	564	0.2483	10146	X-RAY DIFFRACTION	100
3.04-3.12	0.2833	561	0.2493	10183	X-RAY DIFFRACTION	100
3.12-3.21	0.2521	578	0.2443	10183	X-RAY DIFFRACTION	100
3.21-3.32	0.241	453	0.2354	10272	X-RAY DIFFRACTION	100
3.32-3.44	0.2481	586	0.2218	10151	X-RAY DIFFRACTION	100
3.44-3.57	0.24	625	0.2106	10091	X-RAY DIFFRACTION	100
3.57-3.74	0.2136	495	0.1968	10281	X-RAY DIFFRACTION	100
3.74-3.93	0.195	538	0.176	10144	X-RAY DIFFRACTION	100
3.93-4.18	0.1852	575	0.1657	10176	X-RAY DIFFRACTION	100
4.18-4.5	0.1719	485	0.151	10276	X-RAY DIFFRACTION	100
4.5-4.95	0.1604	537	0.1424	10195	X-RAY DIFFRACTION	100
4.95-5.67	0.1754	535	0.1602	10221	X-RAY DIFFRACTION	100
5.67-7.14	0.1951	501	0.1863	10240	X-RAY DIFFRACTION	100
7.14-43.77	0.1947	522	0.1719	9992	X-RAY DIFFRACTION	98

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	0.244	0.2191	-0.0833	0.5379	-0.2268	0.2978	-0.1028	0.0006	-0.0331	-0.1151	0.0695	-0.0154	0.1341	-0.0243	0	0.2186	-0.0326	0.023	0.2359	-0.0054	0.2757	-45.917	-2.3646	-112.8377
2	0.3933	-0.0137	-0.1365	0.1897	0.1223	0.1484	-0.1844	-0.1267	-0.155	-0.118	0.0741	-0.1228	0.2457	0.0584	0	0.3242	0.0575	0.0777	0.2571	0.0556	0.3631	-36.7558	-17.5787	-101.5067
3	0.2985	-0.1076	0.0003	0.1453	-0.2599	0.1802	-0.0858	-0.0513	0.0521	0.2618	0.134	-0.0704	-0.2082	-0.1176	0	0.2893	0.1042	0.0008	0.2174	-0.0173	0.2278	-50.073	77.6847	-90.1531
4	0.0813	-0.0283	-0.0968	0.3091	-0.1372	0.1939	-0.0242	0.0295	0.0137	-0.0018	-0.0025	0.0022	-0.0813	0.0234	0	0.1606	0.0111	0.0253	0.2357	0.0057	0.2377	-40.9605	67.0039	-111.4574
5	0.3803	0.1613	0.0477	0.3001	0.0767	0.1958	-0.1078	0.1078	0.2421	0.0849	0.0038	-0.2223	-0.1679	0.0294	0	0.2699	-0.0308	-0.0224	0.2265	0.0654	0.3614	-37.0778	87.8817	-111.935
6	0.143	-0.0105	0.0488	0.8721	0.0595	0.331	-0.0062	-0.0165	-0.0234	-0.2029	0.0077	0.0206	0.0556	-0.0337	0	0.2243	-0.0276	-0.0205	0.2731	-0.009	0.226	-46.8745	21.8195	-141.683
7	0.3382	-0.0148	-0.0941	0.2652	-0.0793	0.2324	0.0186	0.0168	-0.105	-0.3177	-0.0404	-0.0782	0.0977	0.0231	0	0.3846	-0.0094	0.0273	0.2419	-0.0508	0.2626	-38.3155	4.4829	-149.7705
8	0.2148	0.0326	0.1381	0.5989	0.0101	0.151	0.0658	0.0285	-0.0894	0.4076	0.0039	0.0603	-0.059	-0.0119	-0	0.342	0.012	0.0867	0.2207	0.0094	0.1877	-49.132	44.0002	-63.6813
9	0.1257	0.0546	0.0083	0.2736	-0.1073	0.2033	0.0217	0.0662	-0.011	0.1417	-0.0264	0.0298	-0.1237	-0.0034	0	0.2779	0.0125	0.0259	0.2606	-0.0133	0.2448	-40.2033	54.6621	-82.6726
10	0.0426	0.0136	-0.1702	0.1552	0.0431	0.0597	-0.0415	0.0759	0.0825	0.4548	0.0398	-0.1097	-0.1265	0.0116	0	0.4326	0.0214	0.0301	0.2388	-0.0148	0.2575	-40.9002	71.3437	-64.5216
11	0.0895	-0.0486	-0.0485	0.1633	-0.019	0.0297	0.071	0.0583	-0.0791	0.4805	-0.0173	-0.2718	-0.0404	-0.0412	-0	0.4693	-0.018	-0.1173	0.2733	-0.0119	0.2557	-27.9377	54.5379	-62.2114
12	0.25	0.0048	0.0216	0.3421	0.2567	0.1443	-0.0187	0.0274	-0.0972	0.1334	-0.0367	0.0383	0.1824	-0.002	-0	0.2465	-0.0276	0.0685	0.2543	0.0351	0.2936	-49.7688	-0.2761	-78.0834
13	0.2697	0.046	-0.1045	0.891	0.0865	0.1716	0.0048	-0.0027	-0.0388	0.2909	-0.0211	-0.0869	-0.0561	-0.0077	-0	0.249	-0.0044	-0.0184	0.2159	0.022	0.1956	-37.9494	17.5752	-65.9436
14	0.1653	-0.1249	0.0223	0.2397	0.2973	0.1903	0.0078	-0.0247	0.1188	-0.1821	-0.0437	0.0674	-0.2609	-0.0196	-0	0.2987	0.0543	-0.0442	0.2898	0.0312	0.3019	-50.9427	70.6162	-134.9734
15	0.1447	-0.1366	0.0889	0.2661	-0.0471	0.1725	0.0013	-0.0024	-0.0183	-0.1488	0.0058	-0.0123	-0.0011	-0.0159	-0	0.2154	0.0119	0.0124	0.2505	0.0191	0.2006	-41.6897	46.7711	-136.212
16	0.1299	0.1553	-0.1754	0.3913	-0.0281	0.2231	-0.012	0.008	0.0726	-0.4453	0.0248	-0.0857	-0.057	-0.0187	-0	0.4124	-0.0224	0.0324	0.2479	0.0354	0.1821	-38.2068	56.5545	-154.7056

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 289 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 290 through 495 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 6 through 154 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 155 through 289 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 290 through 495 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 6 through 291 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 292 through 495 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 6 through 172 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 173 through 289 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 290 through 430 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 431 through 495 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 6 through 153 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 154 through 495 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 6 through 154 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 155 through 289 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 290 through 495 )

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Experimental details

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