PDB-8s39: Crystal structure of Medicago truncatula glutamate dehydrogenase ...

ID or keywords:

Entry

Database: PDB / ID: 8s39

Title

Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with isophthalic acid and NAD

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / glutamate dehydrogenase / nitrogen metabolism / inhibitor / NAD / isophthalic acid

Function / homology

Function and homology information

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

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Grzechowiak, M. / Ruszkowski, M.

Funding support

Poland, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2024
Title: Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.
Authors: Grzechowiak, M. / Sliwiak, J. / Link, A. / Ruszkowski, M.

History

Deposition	Feb 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 4, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s39.cif.gz	518.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8s39.ent.gz	404.9 KB	Display	PDB format
PDBx/mmJSON format	8s39.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/s3/8s39 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/8s39	HTTPS FTP

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Related structure data

Related structure data	8s38C 8s3aC 8s3bC 8s3cC 8s3dC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/VR77XI / Data set type: diffraction image data / Metadata reference: 10.18150/VR77XI

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

hetero molecules

138 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	94.728, 162.769, 216.988
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁
Space group name Hall	I2b2c
Symmetry operation	#1: x,y,z #2: x,-y,-z+1/2 #3: -x+1/2,y,-z #4: -x,-y+1/2,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1 #7: -x+1,y+1/2,-z+1/2 #8: -x+1/2,-y+1,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-807- NA
2	1	A-1830- HOH
3	1	A-1850- HOH
4	1	A-1855- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	Glutamate dehydrogenase Mass: 44894.016 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: SNA derive from vector / Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11433210, MTR_5g013470, MtrunA17_Chr5g0399821 / Production host: Escherichia coli (E. coli) / References: UniProt: G7JYL4

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Non-polymers , 8 types, 538 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#8: Chemical	ChemComp-8G0 / benzene-1,3-dicarboxylic acid Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 517 / 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: 3.07 Å³/Da / Density % sol: 59.97 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M Ammonium acetate 0.1 M Sodium acetate 5.0 20 % w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2→81.83 Å / Num. obs: 112829 / % possible obs: 99.8 % / Redundancy: 8.85 % / B_iso Wilson estimate: 42.26 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.092 / R_rim(I) all: 0.097 / Net I/σ(I): 14.66
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 8.45 % / R_merge(I) obs: 1.461 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 17959 / CC_1/2: 0.585 / R_rim(I) all: 1.556 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→81.38 Å / SU ML: 0.2468 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.0745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2124	1128	1 %
R_work	0.1626	111684	-
obs	0.1631	112812	99.84 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.1 Å²

Refinement step

Cycle: LAST / Resolution: 2→81.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9518	0	65	517	10100

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0103	9792
X-RAY DIFFRACTION	f_angle_d	1.0469	13259
X-RAY DIFFRACTION	f_chiral_restr	0.0588	1470
X-RAY DIFFRACTION	f_plane_restr	0.0076	1725
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6023	3649

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 (%)
2-2.09	0.316	139	0.2834	13713	X-RAY DIFFRACTION	98.92
2.09-2.2	0.2754	140	0.2291	13847	X-RAY DIFFRACTION	100
2.2-2.34	0.2533	140	0.2078	13880	X-RAY DIFFRACTION	99.97
2.34-2.52	0.2424	140	0.1874	13915	X-RAY DIFFRACTION	99.99
2.52-2.77	0.2431	141	0.181	13903	X-RAY DIFFRACTION	100
2.77-3.18	0.2053	141	0.1814	13970	X-RAY DIFFRACTION	99.98
3.18-4	0.1813	142	0.1525	14067	X-RAY DIFFRACTION	99.99
4-81.38	0.2036	145	0.1314	14389	X-RAY DIFFRACTION	99.83

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	7.64779952717	4.7059021149	-3.48103547498	5.00585578386	-4.5521532122	4.33683070756	0.560489150343	-0.861868054058	-0.543490255008	0.885806618218	-0.240628406894	-0.162752831406	-0.162457691498	0.0386540322749	-0.463323958244	0.540791725386	-0.0162510822578	-0.0632248438173	0.489468570592	0.121268618555	0.496692902237	53.2442051607	99.8536985597	175.939436875
2	1.40053199525	-1.09177082141	0.344033278607	3.64615720602	-0.154724691486	0.661374362047	-0.0846380587728	-0.215940192145	0.041455825738	0.218413130821	0.0555408089527	0.151149485207	-0.0510336044495	-0.0676829554698	0.0287283448054	0.305952609311	-0.00077520312036	0.0192006775256	0.368873690164	0.00390526696649	0.298021029691	36.4237750651	117.583063353	165.824000947
3	1.28406252936	0.517575677085	-0.199922853006	6.42425112739	-0.20507018562	1.05318340389	0.100564035717	-0.163905710713	-0.0496689575393	-0.0150967973868	-0.0398698051727	0.292636608848	0.00175166970298	0.0736753884133	-0.0654063087684	0.291916748022	0.0152506823829	-0.0286032735876	0.370119364192	-0.0127779427139	0.352085105426	28.389507906	114.588995223	154.263739849
4	3.75938806662	-0.161201102559	0.329937418911	2.71461363401	-0.0390814366521	3.54672516503	0.077554228003	-0.537759781791	-0.0436387105328	0.278602015497	-0.0168386432946	0.402756319419	-0.1117067411	-0.557644011365	-0.0606037223347	0.413700792992	0.00519460895947	0.0923846116491	0.509026533472	0.0709262263343	0.449776775143	18.2189450348	92.0453908345	176.874444561
5	1.45492351517	-0.282864669708	0.899644222982	1.56885857208	-2.36465758167	6.3470354559	0.0984940349177	-0.221241360778	-0.140483541296	0.158640128026	-0.032359895549	0.0808571030254	-0.0556160726305	0.158515418864	0.200930382422	0.388138363358	-0.00590605293786	0.045141960693	0.372814621477	0.0192515356063	0.43702787851	32.375545845	96.8019892937	168.286025798
6	4.63786284085	-5.34636313004	3.00600745626	6.7865305105	-4.6157571341	4.03779427098	0.0851913787738	-0.0784072290722	-0.318478241186	-0.0239133131646	0.0291819676979	0.0688146150199	0.119477270463	-0.0657366338475	-0.622670039529	0.366147533616	-0.000972725420611	0.0214202715204	0.324092682603	0.0250288031528	0.415942439352	34.6707039212	89.1644909873	161.808960196
7	9.06034148678	6.56047391501	-7.30433372956	5.46712889243	-5.75483071194	7.92141554829	0.211389622351	-0.159614762489	-0.139085654534	0.121728151994	-0.0906137688005	-0.0299708890684	-0.0209756877419	0.196634400363	-0.0492054585515	0.399896260288	0.0345614372561	-0.0237767089788	0.388796373282	0.0554744632503	0.38585448898	49.8566892979	96.3220222528	167.216316315
8	1.00369165036	-0.0200375063018	-0.525132758548	0.457804913059	-0.0105323868977	0.686809863501	0.0503076130877	0.0823293009046	0.0392368642744	-0.0552694340825	-0.0613750639133	0.0647242774795	-0.0680014665729	-0.11695743415	-0.0108851331299	0.370121386705	0.0361936738312	-0.0312406449175	0.40833513968	-0.0134827692575	0.379992939616	27.7004223292	119.349938423	128.494543001
9	1.13726207796	0.241597880391	0.567848403572	1.09348435136	0.584125095849	1.16994409207	-0.028736487876	0.114873467464	-0.0187971860675	-0.107488625587	0.00644839118223	0.0915076383846	0.0759584061813	-0.0734799381255	0.0417462426232	0.345012217168	-0.0147722341698	-0.00429880263733	0.335390921557	0.0397295859676	0.342507699229	9.80055244595	103.289942096	127.242045407
10	1.84653714666	0.460410484706	1.75788349505	0.92218849784	0.897895958444	4.19143865497	-0.0704032840461	0.111991516136	-0.0312330397396	-0.14431783001	-0.00661207560871	-0.13445498152	-0.0549987131538	0.205116682947	0.0621648204456	0.310656734671	0.0462609188388	0.0520212671012	0.320598932097	0.0496818149456	0.366938018511	64.0150716964	102.143223348	129.78066054
11	1.79360195368	1.08568051426	1.73021308646	0.838073045844	1.33207414797	3.88835080641	0.102481361286	0.12106542025	-0.0786538969923	-0.00838723912355	-0.0326268005879	-0.159131436169	0.140556526351	0.241379196998	-0.161840594464	0.364126358288	0.0634497090356	-0.00768714021394	0.334036088653	0.0570905630649	0.380705790587	60.988610475	97.6615232619	133.982158237
12	5.25582716046	1.53086358063	1.26193128385	2.31197496239	0.786490364822	1.85315813457	0.0437874519546	-0.200669538611	0.19777894013	0.0754905131782	-0.122304866616	0.0137541173379	0.0642667850561	-0.0313863975982	0.0897071936899	0.28460153108	0.0368800339797	0.021101698585	0.302850689409	0.0249699606802	0.286888548714	57.050569858	102.869458299	147.299734077
13	2.1931775744	-0.0511682135598	0.255115885981	1.25212471647	-0.415081827899	3.0475580824	0.0481241077485	-0.0503964039211	-0.338090697052	-0.0627516152482	-0.144214677952	-0.283383175609	0.450590367387	0.233719918702	0.0755105860342	0.434822025818	0.0650731672112	0.0301713432099	0.335034378718	0.0524103354962	0.46751187809	64.8089101899	75.3287587754	137.2752424
14	7.36411513206	-5.76912924507	-5.49721779394	5.69777112535	4.77190615223	4.74387762486	0.1224564343	0.123261922854	-0.0454064060976	-0.151920389003	-0.0965879296094	-0.100210428793	0.0700516065649	0.100251470316	-0.0168914860716	0.318916016291	0.0455444185971	-0.0108092659914	0.292548186415	0.0587911079174	0.313398537904	54.7250599122	88.3985456147	132.088418794
15	3.02799462239	-1.81797599731	0.585230016193	7.11423475131	4.29672195222	3.69717601667	-0.145264114646	-0.0322599028998	-0.208565450283	-0.0149796196613	-0.133821679348	0.428257016704	0.413216894471	-0.162795273646	0.327136583927	0.290865734871	0.0146750202587	-0.0421245242939	0.324323013332	-0.00310934577664	0.426105546967	44.4899175616	84.4794034572	129.496795904
16	8.52252018803	-6.55694614156	-0.480841655753	8.87576296357	-0.676279214997	1.60366857228	-0.0573813206178	0.0957357689587	-0.0800813363222	-0.350222769627	0.026413456488	0.0680664810497	0.0706197255536	0.00605250285381	0.0982142518946	0.329033182058	0.0347531278013	-0.0163574532974	0.364539638794	-0.0150861883598	0.205778763694	50.1161508422	97.4849607253	118.856455107

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 146 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 147 through 183 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 184 through 308 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 309 through 358 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 359 through 384 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 385 through 411 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 183 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 184 through 411 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -1 through 76 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 77 through 113 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 114 through 183 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 184 through 308 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 309 through 358 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 359 through 384 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 385 through 411 )

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