PDB-8ysw: phosphinothricin dehydrogenase

ID or keywords:

Entry

Database: PDB / ID: 8ysw

Title

phosphinothricin dehydrogenase

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / Crystal Structure of phosphinothricin dehydrogenase with cofactor

Function / homology

Function and homology information

glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / nucleotide binding
Similarity search - Function

Biological species

Lysinibacillus composti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.61 Å

Authors

Xue, Y.P. / Cheng, F. / Zhou, S.P. / Xu, J.M. / Jin, L.Q. / Ma, C.J. / Zheng, Y.G.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of phosphinothricin dehydrogenase with NAD at 2.6 Angstorms resolution
Authors: Xue, Y.P. / Cheng, F. / Zhou, S.P. / Xu, J.M. / Jin, L.Q. / Zheng, Y.G.

History

Deposition	Mar 23, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ysw.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8ysw.ent.gz	756.1 KB	Display	PDB format
PDBx/mmJSON format	8ysw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ysw_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8ysw_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8ysw_validation.xml.gz	95.9 KB	Display
Data in CIF	8ysw_validation.cif.gz	124.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/8ysw ftp://data.pdbj.org/pub/pdb/validation_reports/ys/8ysw	HTTPS FTP

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Related structure data

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

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

F: Glutamate dehydrogenase

hetero molecules

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

1

A: Glutamate dehydrogenase

F: Glutamate dehydrogenase

hetero molecules

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

hetero molecules

defined by author&software
279 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.665, 129.068, 219.138
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Glutamate dehydrogenase Mass: 45839.148 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysinibacillus composti (bacteria) / Gene: EBB45_13425 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N9UCW8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H₂O
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: 2.51 Å³/Da / Density % sol: 50.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis Tris Propane, pH 6.5, 0.2 M Sodium malonate dibasic monohydrate, 20% w/v PEG 3350, 10 % v/v Ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.61→48.36 Å / Num. obs: 80621 / % possible obs: 99.95 % / Redundancy: 13.1 % / B_iso Wilson estimate: 46.2 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.1873 / R_pim(I) all: 0.05356 / R_rim(I) all: 0.1949 / Net I/σ(I): 12.55
Reflection shell	Resolution: 2.61→2.703 Å / Redundancy: 13.1 % / R_merge(I) obs: 1.379 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 7955 / CC_1/2: 0.752 / CC star: 0.927 / R_pim(I) all: 0.3954 / R_rim(I) all: 1.435 / R_sym value: 1.379 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHASES		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.61→48.36 Å / SU ML: 0.3602 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2571	3956	4.91 %
R_work	0.1924	76651	-
obs	0.1956	80607	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 49.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.61→48.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18297	0	256	370	18923

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	18894
X-RAY DIFFRACTION	f_angle_d	0.9523	25578
X-RAY DIFFRACTION	f_chiral_restr	0.0556	2874
X-RAY DIFFRACTION	f_plane_restr	0.0085	3286
X-RAY DIFFRACTION	f_dihedral_angle_d	16.5899	7044

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 (%)
2.61-2.64	0.3236	151	0.253	2716	X-RAY DIFFRACTION	100
2.64-2.68	0.3348	153	0.2478	2665	X-RAY DIFFRACTION	100
2.68-2.71	0.3495	133	0.2505	2721	X-RAY DIFFRACTION	99.96
2.71-2.75	0.3056	126	0.2271	2712	X-RAY DIFFRACTION	100
2.75-2.79	0.3032	146	0.2236	2713	X-RAY DIFFRACTION	99.97
2.79-2.83	0.2785	145	0.2141	2686	X-RAY DIFFRACTION	100
2.83-2.87	0.2997	122	0.2127	2705	X-RAY DIFFRACTION	100
2.87-2.92	0.363	135	0.2342	2722	X-RAY DIFFRACTION	100
2.92-2.97	0.3058	126	0.2309	2740	X-RAY DIFFRACTION	100
2.97-3.02	0.3228	151	0.2375	2680	X-RAY DIFFRACTION	99.93
3.02-3.08	0.2856	134	0.2313	2738	X-RAY DIFFRACTION	100
3.08-3.15	0.2791	141	0.2329	2696	X-RAY DIFFRACTION	100
3.15-3.21	0.3061	152	0.2282	2713	X-RAY DIFFRACTION	99.97
3.21-3.29	0.3479	140	0.2146	2690	X-RAY DIFFRACTION	100
3.29-3.37	0.309	134	0.2085	2738	X-RAY DIFFRACTION	100
3.37-3.46	0.3114	132	0.2078	2752	X-RAY DIFFRACTION	99.97
3.46-3.56	0.2365	111	0.201	2755	X-RAY DIFFRACTION	100
3.56-3.68	0.2587	133	0.1942	2728	X-RAY DIFFRACTION	100
3.68-3.81	0.2455	149	0.1948	2725	X-RAY DIFFRACTION	100
3.81-3.96	0.2634	151	0.1731	2715	X-RAY DIFFRACTION	100
3.96-4.14	0.2174	146	0.1624	2742	X-RAY DIFFRACTION	100
4.14-4.36	0.2073	133	0.154	2761	X-RAY DIFFRACTION	100
4.36-4.63	0.1974	150	0.1476	2773	X-RAY DIFFRACTION	100
4.63-4.99	0.2182	163	0.16	2728	X-RAY DIFFRACTION	100
4.99-5.49	0.2268	148	0.1703	2775	X-RAY DIFFRACTION	100
5.49-6.29	0.2631	154	0.1987	2781	X-RAY DIFFRACTION	100
6.29-7.91	0.2273	127	0.1847	2846	X-RAY DIFFRACTION	100
7.91-48.36	0.2262	170	0.1813	2935	X-RAY DIFFRACTION	99.62

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	0.930221872979	-0.520102158347	0.295989366297	1.23876456167	-0.392076704094	0.928986286795	-0.00520640272022	0.0385098551899	0.0711799709251	-0.089314847898	-0.0541551261552	-0.199799778928	-0.0457376258335	0.145733796084	0.0379794457459	0.32649149236	-0.0278359587956	0.0509847545506	0.348196420408	0.0375507069201	0.379676133779	-0.385791705695	-41.8733282433	18.6184657889
2	2.11021765478	0.292271642115	-1.19520726167	2.90910801084	-1.11818289912	2.50604285098	0.206475285825	-0.333771908334	0.230537983487	0.252037784104	-0.318357770112	-0.374289477513	-0.495046962057	0.35936483267	0.0778653551689	0.479359965367	-0.163648425304	-0.0329745313007	0.460880719022	0.00159126598529	0.387659971521	19.1247823217	-16.6868390161	23.7300248521
3	0.871719008421	0.396987012002	-0.166139595541	1.49233243774	-0.947803846691	0.564413798522	0.020692175474	-0.158560771293	-0.0140299924437	0.148124459377	-0.193379520286	-0.169769204382	-0.181186279584	0.2231126198	0.146594057801	0.410834054718	-0.0819941369159	-0.0218521544907	0.510444012521	0.0110724836819	0.395199082939	8.62562137677	-34.5060901611	35.2459933775
4	0.628459053761	-0.187559320679	-0.353673322097	1.3235250186	-0.597616619275	1.31557550961	-0.0038278837966	-0.126772483132	0.149969024825	0.177888224222	-0.0778763511174	-0.21640524532	-0.213494439329	0.251820729331	0.0740226847152	0.355304230052	-0.055068637696	-0.0736870911921	0.352829084665	0.0128516288353	0.409986134479	43.8374627184	1.33539350211	-14.322032462
5	2.5597738451	-0.708610659095	-0.550105304318	0.455390342579	1.03703896626	3.25680740885	0.342572739229	0.0175925470833	0.465496564257	0.664812525504	-0.184123678963	-0.37002491215	-0.492306004743	-0.0624950640283	-0.161830190343	0.852161944528	-0.198615061614	-0.120400521971	0.310263950917	-0.0296119340789	0.610564990143	35.4148993226	20.7211154758	-3.73474678377
6	3.53041790208	-0.556894270155	1.02956440012	3.16344114677	-0.565657895517	3.92695908394	0.862717746432	-0.542203649383	-0.00323600794941	0.570240145407	-0.357923126062	-0.349913560675	-0.425951323274	0.871069253554	-0.464524634593	1.43642074171	-0.266059237805	-0.221258401637	0.802185334768	0.0552199492192	0.731358546482	47.3059373724	14.7125285446	12.1871068551
7	1.06085356403	0.51917884363	0.548524230098	2.2504968425	-0.49302783618	1.84141304019	-0.0055194313799	-0.285876003574	0.271925309414	0.609084479234	-0.10679443436	-0.0670223025249	-0.4965970633	0.0433262846894	0.0896857501599	0.544519140226	-0.0509067404021	-0.010573483423	0.46170655042	-0.0348257115341	0.407694368879	31.756958531	8.53980445037	-0.163712478873
8	0.743707193938	0.408315290516	-0.0137310229663	1.75928561063	-0.0269732716468	0.94665300372	0.0587966401598	0.10075009815	0.103368656373	0.0659995533996	-0.0386445925971	0.0405876863084	-0.144051902034	-0.109337044426	-0.0224839924539	0.323794078943	0.0152257759596	-0.0180227244034	0.348844703101	0.047986400435	0.388941793398	14.7923145743	8.45066031684	-39.5381457661
9	3.65660801608	-1.62550169533	-0.0708276475354	1.55309662014	0.107427385694	1.72670542317	0.0199647232095	0.0276986159664	-0.24117221055	-0.0321866502278	-0.0160329129378	0.362521405701	-0.116689365867	-0.371159005592	-0.00594608346281	0.408461801786	-0.0308005325189	-0.0245616276824	0.399720092611	0.0127235560798	0.538753598434	-0.981658418851	32.7231583963	-39.0677819676
10	1.48421389586	-0.288089215186	-0.252019308218	2.2246957803	0.460373515732	2.17906879527	0.141354845479	0.414292009343	-0.00465049266636	-0.287386260962	0.157211086864	-0.0648005784022	-0.0640314685734	-0.215439228889	-0.262981088223	0.379001973367	0.0240511585831	0.00095585221257	0.52396861741	0.0525297678886	0.54958294365	13.1104020869	35.3166905255	-44.7106068665
11	0.30351121808	0.148445529935	0.133830060341	2.24608400696	-0.800707658593	0.990351932184	-0.132229654525	-0.101492359984	0.124299331879	0.35208944831	0.14069205258	-0.165149961355	-0.115600524494	-0.0648050814345	-0.0543672010384	0.373869047056	0.0362929146708	0.00342697489444	0.408026332914	-0.0177437809566	0.412701347007	14.6753650974	23.4176690811	-25.6564191488
12	1.52055490686	-1.8852262543	0.445178733933	2.82312970189	-1.23042098527	1.00190258428	0.140508301761	-0.218406449158	0.293442839339	-0.0889302972262	-0.305636211267	-0.481558106644	0.00775859595975	0.0199657118334	0.12546436794	0.349411984708	-0.0888510802712	-0.0245337927871	0.363298257196	0.0230750239719	0.427159597651	29.8502901116	23.2627714085	-35.0043134285
13	1.04910807429	0.0585611732978	-0.0455863385582	0.97650387971	-0.149827980137	0.584114630014	0.051922024409	0.175456540396	-0.0676047886009	-0.138376379346	-0.018753316753	0.0725648482055	0.0391487494752	-0.0816910160089	-0.0117796956668	0.331851420072	0.0180652861824	-0.0109148413065	0.412216079292	-0.0476523476278	0.343448663424	14.1899672493	6.23646045686	58.8817651251
14	3.29536486079	-0.215940920081	0.301064551506	0.729296052362	0.626107907268	1.69005646568	-0.350548611887	0.149081907672	0.401619221062	-0.00357100604794	0.0370894152921	0.283011699249	0.0871275125503	0.0875837956175	0.273629947853	0.489144204478	0.124823860767	-0.034527916046	0.432279641058	-0.013215423025	0.469648817889	-0.113459328246	26.3303360238	33.7267923233
15	1.46261211368	-0.400740604432	1.0191453781	1.20353249959	0.705815432513	1.55280173554	0.102280816009	0.445915157324	-0.0017975271554	-0.29806589529	-0.0404409657406	-0.214668172388	0.054480019238	0.484790958378	-0.0708651604843	0.408618628475	0.0203181307022	-0.00665716494306	0.699042867121	0.0140432617547	0.454068525738	13.602919542	19.2626381332	30.0813134336
16	0.379383366091	0.308905532252	-0.40826355154	0.359431113588	0.0205079604961	1.73063983075	0.0240932702367	0.03888620006	0.252069666973	-0.0302765914531	0.00803326999686	0.0351486570989	-0.167160728636	-0.240797317041	-0.0124976572954	0.344605666247	0.0286947115961	-0.0177882142887	0.384826390864	-0.022348472896	0.386607132647	19.1863056125	24.6071743273	53.2273255104
17	0.999273838869	-0.552460084109	-0.191630161246	1.42518808957	0.714517594017	1.52542546321	-0.0205299481032	0.0766299490534	0.0616730099628	0.0417767202469	0.00188956618179	-0.0839981400129	-0.173574549956	0.163186776756	0.0105643606058	0.370370334244	-0.0434000615431	0.00883236687963	0.345243122505	0.0236028987159	0.362674738128	36.997619598	29.3861896131	80.3652438053
18	1.35170348197	0.296583132446	-1.0109695439	1.6350861162	0.013088776429	2.44047511653	0.0915592689294	-0.180874031514	0.24182990226	-0.0165194955038	0.00637875010933	-0.129393457237	-0.337266698446	0.384160316286	-0.0768263427392	0.476851417975	-0.0405783559336	0.0462277497938	0.383615522425	0.0222961177681	0.420683382528	43.9925602398	52.1651665741	70.0492337244
19	0.689918319253	-0.0072801216833	0.170965907749	1.68271425663	0.927081673546	0.590564814111	-0.000452095126731	0.0600227381633	0.0599786779609	-0.22851246206	0.00242184950721	-0.0874469617109	-0.353129514974	-0.160249998077	0.0247252286015	0.438357552458	0.00870731436741	0.0296264457868	0.384270536798	0.0221614504788	0.39598406785	23.633496436	42.8372032976	78.8725019504
20	1.17692330561	-0.175611416825	0.825979453735	1.11015221017	-0.193112789291	1.56188394843	0.0360464125782	-0.145430937232	-0.0288484704616	0.201167057333	-0.00602234920034	0.096117183522	0.108319554572	-0.110034038879	-0.038265920423	0.375606233067	-0.0177256351399	0.0336532346554	0.328125962816	0.00975036381542	0.296461428372	9.19558373096	-14.6690124581	-8.68878500687
21	1.76629996944	-0.0422202062136	-1.05649908888	0.359804124322	-0.0533862462979	2.59236763004	-0.0259016787067	-0.298239812571	0.109761445824	0.168863826674	0.0413755852729	0.0987816667839	-0.137965961296	-0.0961795530594	0.00133641228822	0.488477381805	0.0377185901218	0.0518140991135	0.3577477467	0.0265350772527	0.398440608342	-5.35565586776	1.53922167833	5.07031252407

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid -1 through 182 )	C	J	-1 - 182	1 - 184
2	2	chain 'C' and (resid 183 through 314 )	C	J	183 - 314	185 - 316
3	3	chain 'C' and (resid 315 through 408 )	C	J	315 - 408	317 - 410
4	4	chain 'D' and (resid -1 through 174 )	D	M	-1 - 174	1 - 176
5	5	chain 'D' and (resid 175 through 196 )	D	M	175 - 196	177 - 198
6	6	chain 'D' and (resid 197 through 330 )	D	M	197 - 330	199 - 226
7	7	chain 'D' and (resid 331 through 408 )	D	M	331 - 408	227 - 304
8	8	chain 'E' and (resid -4 through 182 )	E	N	-4 - 182	1 - 187
9	9	chain 'E' and (resid 183 through 298 )	E	N	183 - 298	188 - 303
10	10	chain 'E' and (resid 299 through 323 )	E	N	299 - 323	304 - 328
11	11	chain 'E' and (resid 324 through 382 )	E	N	324 - 382	329 - 387
12	12	chain 'E' and (resid 383 through 408 )	E	N	383 - 408	388 - 413
13	13	chain 'F' and (resid -1 through 182 )	F	Q	-1 - 182	1 - 184
14	14	chain 'F' and (resid 183 through 271 )	F	Q	183 - 271	185 - 273
15	15	chain 'F' and (resid 272 through 336 )	F	Q	272 - 336	274 - 338
16	16	chain 'F' and (resid 337 through 408 )	F	Q	337 - 408	339 - 410
17	17	chain 'A' and (resid -4 through 182 )	A	A	-4 - 182	1 - 187
18	18	chain 'A' and (resid 183 through 335 )	A	A	183 - 335	188 - 340
19	19	chain 'A' and (resid 336 through 410 )	A	A	336 - 410	341 - 415
20	20	chain 'B' and (resid -1 through 182 )	B	F	-1 - 182	1 - 184
21	21	chain 'B' and (resid 183 through 408 )	B	F	183 - 408	185 - 410

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