PDB-9yis: Crystal structure of glutamate dehydrogenase from Babesia microti

ID or keywords:

Entry

Database: PDB / ID: 9yis

Title

Crystal structure of glutamate dehydrogenase from Babesia microti

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / glutamate dehydrogenase / Babesia microti

Function / homology

Function and homology information

glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol
Similarity search - Function

Biological species

Babesia microti strain RI (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of glutamate dehydrogenase from Babesia microti
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Oct 2, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yis.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9yis.ent.gz	891 KB	Display	PDB format
PDBx/mmJSON format	9yis.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9yis_validation.pdf.gz	504.6 KB	Display	wwPDB validaton report
Full document	9yis_full_validation.pdf.gz	528 KB	Display
Data in XML	9yis_validation.xml.gz	114.2 KB	Display
Data in CIF	9yis_validation.cif.gz	146.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yi/9yis ftp://data.pdbj.org/pub/pdb/validation_reports/yi/9yis	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

321 kDa, 6 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)	154.068, 197.300, 229.680
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-691- HOH

#1: Protein	Glutamate dehydrogenase Mass: 53301.367 Da / Num. of mol.: 6 / Fragment: 2-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Babesia microti strain RI (eukaryote) / Gene: BMR1_03g03380 / Plasmid: BamiA.17991.a.A21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K3AUK4
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.73 Å³/Da / Density % sol: 54.93 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% 3350, 0.1M BT 6.5, 0.2M sodium acetate. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 D3 drop1, Puck: PSL-0516, Cryo: 12.5% ...Details: 25% 3350, 0.1M BT 6.5, 0.2M sodium acetate. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 D3 drop1, Puck: PSL-0516, Cryo: 12.5% P200 + 87.5% crystallant.

Crystal

Density Matthews: 2.73 Å³/Da / Density % sol: 54.93 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% 3350, 0.1M BT 6.5, 0.2M sodium acetate. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 D3 drop1, Puck: PSL-0516, Cryo: 12.5% ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 25, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.18→49.63 Å / Num. obs: 181027 / % possible obs: 100 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.178 / R_pim(I) all: 0.05 / R_rim(I) all: 0.185 / Χ²: 1.07 / Net I/σ(I): 12.9 / Num. measured all: 2475202
Reflection shell	Resolution: 2.18→2.24 Å / % possible obs: 100 % / Redundancy: 14 % / R_merge(I) obs: 1.83 / Num. measured all: 186105 / Num. unique obs: 13326 / CC_1/2: 0.691 / R_pim(I) all: 0.506 / R_rim(I) all: 1.899 / Χ²: 0.97 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5438: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.18→48.58 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2094	9003	4.98 %
R_work	0.1827	-	-
obs	0.1841	180928	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.18→48.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21488	0	88	694	22270

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	22010
X-RAY DIFFRACTION	f_angle_d	0.708	29680
X-RAY DIFFRACTION	f_dihedral_angle_d	12.051	8092
X-RAY DIFFRACTION	f_chiral_restr	0.045	3226
X-RAY DIFFRACTION	f_plane_restr	0.006	3882

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 (%)
2.18-2.2	0.3216	308	0.2852	5657	X-RAY DIFFRACTION	100
2.2-2.23	0.2694	293	0.2638	5711	X-RAY DIFFRACTION	100
2.23-2.26	0.3025	288	0.2635	5674	X-RAY DIFFRACTION	100
2.26-2.29	0.3102	299	0.2527	5690	X-RAY DIFFRACTION	100
2.29-2.32	0.2837	310	0.2411	5723	X-RAY DIFFRACTION	100
2.32-2.35	0.2632	297	0.2301	5667	X-RAY DIFFRACTION	100
2.35-2.38	0.2743	297	0.2335	5662	X-RAY DIFFRACTION	100
2.38-2.42	0.2556	297	0.2393	5728	X-RAY DIFFRACTION	100
2.42-2.46	0.2388	288	0.2207	5697	X-RAY DIFFRACTION	100
2.46-2.5	0.2666	315	0.2279	5698	X-RAY DIFFRACTION	100
2.5-2.54	0.2412	293	0.2223	5694	X-RAY DIFFRACTION	100
2.54-2.58	0.2736	268	0.2152	5716	X-RAY DIFFRACTION	100
2.58-2.63	0.2431	279	0.2079	5729	X-RAY DIFFRACTION	100
2.63-2.69	0.2475	281	0.2006	5705	X-RAY DIFFRACTION	100
2.69-2.75	0.2203	313	0.1939	5697	X-RAY DIFFRACTION	100
2.75-2.81	0.2324	259	0.19	5753	X-RAY DIFFRACTION	100
2.81-2.88	0.2386	296	0.2005	5719	X-RAY DIFFRACTION	100
2.88-2.96	0.2562	323	0.2061	5691	X-RAY DIFFRACTION	100
2.96-3.05	0.2318	306	0.2121	5722	X-RAY DIFFRACTION	100
3.05-3.14	0.2432	307	0.2099	5737	X-RAY DIFFRACTION	100
3.14-3.26	0.2472	311	0.2085	5696	X-RAY DIFFRACTION	100
3.26-3.39	0.2193	320	0.1942	5712	X-RAY DIFFRACTION	100
3.39-3.54	0.1994	316	0.1852	5732	X-RAY DIFFRACTION	100
3.54-3.73	0.223	289	0.173	5754	X-RAY DIFFRACTION	100
3.73-3.96	0.1802	313	0.1654	5761	X-RAY DIFFRACTION	100
3.96-4.27	0.166	302	0.1391	5769	X-RAY DIFFRACTION	100
4.27-4.7	0.1462	323	0.1275	5752	X-RAY DIFFRACTION	100
4.7-5.37	0.1647	300	0.1371	5811	X-RAY DIFFRACTION	100
5.37-6.77	0.1814	302	0.1627	5857	X-RAY DIFFRACTION	100
6.77-48.58	0.1624	310	0.1549	6011	X-RAY DIFFRACTION	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	0.3916	0.099	0.1389	0.5091	-0.0747	0.2835	0.1036	-0.0423	-0.1025	0.008	-0.0327	0.0006	0.0941	-0.1188	0.0004	0.323	-0.0707	-0.0365	0.3733	0.0363	0.355	54.8342	36.8542	28.9271
2	1.2316	0.496	0.2377	0.4263	0.2219	0.8562	-0.0492	-0.0163	0.0116	-0.0821	-0.0529	-0.0173	-0.1357	-0.0329	0	0.3665	-0.0203	-0.0625	0.3139	0.0557	0.4531	36.8528	14.6815	24.8423
3	0.7848	0.2692	0.0291	0.4381	0.165	0.0104	0.1183	-0.1559	-0.3632	0.0358	-0.1261	-0.1685	-0.0506	0.0077	-0	0.4018	-0.082	-0.1037	0.3735	0.0795	0.4291	57.8434	21.7146	34.359
4	0.804	-0.0823	-0.2037	0.5931	0.4521	0.776	0.1315	-0.0553	-0.2406	0.0567	0.0487	-0.2129	0.0491	0.0971	0.0255	0.3305	-0.0062	-0.0713	0.3365	-0.0125	0.4908	96.4535	38.1273	29.9779
5	0.5535	-0.1898	-0.1181	0.3356	-0.0693	1.2009	0.1104	-0.0692	-0.3263	0.2814	0.1209	0.002	0.3973	0.0839	0.6119	0.4862	-0.0066	-0.2158	0.3344	-0.06	0.5724	85.2926	19.8444	32.2808
6	0.5898	0.0659	0.3029	0.0504	-0.2342	1.3028	-0.0996	-0.2046	0.1344	0.3795	0.2863	-0.2492	0.6458	-0.022	-0.0144	0.9654	0.1952	-0.3851	0.493	-0.1049	0.6793	94.5652	7.641	48.4511
7	0.4499	-0.0082	-0.6135	0.5428	0.0791	1.5573	-0.0071	-0.0396	-0.114	0.138	0.155	-0.3877	0.3554	0.3341	0.1116	0.4286	0.0939	-0.2129	0.3679	-0.0937	0.7395	98.7288	18.0428	28.9563
8	1.3329	0.3056	0.369	0.7382	0.0631	0.4543	0.0244	0.1472	-0.1446	-0.1449	0.0852	-0.1389	0.0644	0.0336	-0	0.3732	-0.048	0.0397	0.3568	-0.0594	0.3494	76.1015	34.7669	-4.9552
9	0.9537	-0.3803	0.0834	0.8999	-0.2213	0.6589	0.7822	0.747	-0.142	-0.5595	-0.556	-0.3745	0.2143	0.1424	0.1953	0.7335	0.2198	0.1681	0.7631	-0.1043	0.7076	88.5647	11.8406	-16.5112
10	1.3072	-0.9349	0.4142	0.9728	-0.0083	0.6443	0.1639	0.1969	-0.2489	-0.0704	-0.0445	0.0411	0.1531	0.0481	0	0.4195	-0.0599	-0.0415	0.3818	-0.0397	0.4613	69.6408	19.8686	-3.366
11	1.1496	0.2187	-0.2579	0.6946	-0.0203	0.1206	-0.0803	0.1823	0.1004	-0.177	0.1269	0.0224	-0.087	-0.0247	0	0.3983	-0.0809	0.004	0.377	0.0303	0.2888	74.9875	64.2164	-6.4835
12	2.2413	-1.2846	-0.5225	1.5304	0.0518	0.948	0.1972	0.6321	0.217	-0.3698	-0.1056	0.0608	-0.1504	-0.1396	0.0004	0.4836	-0.1026	-0.0477	0.4738	0.1096	0.3743	70.9064	81.608	-12.8307
13	0.2076	0.1025	0.0493	0.5696	-0.137	0.6863	0.0734	-0.0498	0.104	0.0224	-0.0099	0.0984	-0.1112	-0.1534	0	0.3251	0.0142	0.0313	0.3678	0.0123	0.3111	56.8227	64.4691	29.4654
14	0.8921	0.5057	-0.093	0.8959	1.0152	1.9732	-0.0163	-0.2828	-0.0507	0.2154	-0.0024	-0.0087	-0.5215	-0.5968	0.053	0.6344	0.1826	0.1291	0.593	0.0609	0.4128	53.7473	88.6212	45.8229
15	0.4273	0.047	0.5274	0.2735	-0.036	1.0303	0.0563	0.1123	-0.0417	-0.0723	-0.0894	0.0492	-0.3689	-0.3659	-0.0071	0.4404	0.0803	0.0438	0.4459	0.0027	0.3564	57.7114	79.9505	28.9481
16	0.5195	-0.1058	-0.2676	0.2965	-0.0009	0.5758	0.0161	0.0085	0.0707	-0.2063	0.0387	0.1491	-0.4365	-0.2501	0	0.4902	0.0864	0.0069	0.4233	0.0478	0.4337	53.1292	79.5173	19.1415
17	0.3421	0.0792	0.1008	0.465	0.1055	0.1009	0.0355	-0.0163	-0.0713	0.014	0.0293	-0.1751	-0.0551	0.0772	0	0.326	-0.0643	0.0231	0.3626	-0.0237	0.369	96.6224	62.8522	27.7589
18	1.5386	0.3255	0.7633	0.6292	-0.5088	1.2389	0.0236	0.1605	-0.0234	-0.018	-0.085	-0.0404	0.1743	0.1649	-0	0.3464	-0.0019	0.0277	0.3379	0.0056	0.419	113.9105	86.2107	22.0583
19	0.4301	0.3501	-0.0585	0.6439	0.1542	0.4462	0.0063	-0.0316	0.0912	-0.0156	-0.0364	-0.0208	-0.092	0.0177	0	0.3754	-0.059	0.0221	0.3604	-0.008	0.3373	93.2466	78.6203	32.0143

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 240 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 241 through 371 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 372 through 467 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 201 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 202 through 240 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 241 through 339 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 340 through 467 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 2 through 240 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 241 through 371 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 372 through 467 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 1 through 257 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 258 through 467 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 1 through 240 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 241 through 371 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 372 through 413 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 414 through 467 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 1 through 240 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 241 through 371 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 372 through 467 )

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