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- PDB-5tc3: Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP ... -

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Open data

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Basic information

Entry

Database: PDB / ID: 5tc3

Title

Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP and GDP

Components

Inosine-5'-monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE /

IMP dehydrogenase /

Ashbya gossypii /

allosteric modulator / purine nucleotides

Function / homology

Function and homology information

IMP dehydrogenase activity /

IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process /

nucleotide binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Ashbya gossypii ATCC 10895 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.462 Å

Authors

Fernandez-Justel, D. / de Pereda, J.M. / Revuelta, J.L. / Buey, R.M.

Citation

Journal: Sci Rep / Year: 2017
Title: A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.
Authors: Buey, R.M. / Fernandez-Justel, D. / Marcos-Alcalde, I. / Winter, G. / Gomez-Puertas, P. / de Pereda, J.M. / Luis Revuelta, J.

History

Deposition	Sep 14, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	5tc3.cif.gz	531.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5tc3.ent.gz	447.3 KB	Display	PDB format
PDBx/mmJSON format	5tc3.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/tc/5tc3 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/5tc3	HTTPS FTP

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Related structure data

Related structure data	5mcpC 4z87S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z87-3 4z87-1 4z87-2 6jig-1 20743 6ua4-d 6udo-d 1zfj-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1)

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Assembly

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

117 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by author
468 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	147.880, 147.880, 103.542
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein	Inosine-5'-monophosphate dehydrogenase / IMPDH Mass: 56664.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ashbya gossypii ATCC 10895 (fungus) / Gene: AGOS_AER117W / Production host: Escherichia coli (E. coli) / References: UniProt: Q756Z6, IMP dehydrogenase

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Non-polymers , 5 types, 60 molecules

#2: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.12 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Lithium Acetate 0.1 M BisTris, pH 6.0 20% (w/v) Sokolan CP42

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99987 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 2.46→46.76 Å / Num. obs: 40435 / % possible obs: 99.78 % / Redundancy: 13.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.1446 / Net I/σ(I): 10.64
Reflection shell	Resolution: 2.46→2.55 Å / Redundancy: 13.5 % / R_merge(I) obs: 1.435 / Mean I/σ(I) obs: 1.35 / CC_1/2: 0.711 / % possible all: 99.33

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Processing

Software

Name	Version	Classification
PHENIX	(1.11rc1_2513: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z87

Resolution: 2.462→46.76 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.39

	R_factor	Num. reflection	% reflection
R_free	0.2417	4150	5.24 %
R_work	0.2165	-	-
obs	0.2178	40355	99.71 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.462→46.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7170	0	226	51	7447

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7611
X-RAY DIFFRACTION	f_angle_d	0.561	10350
X-RAY DIFFRACTION	f_dihedral_angle_d	14.05	4477
X-RAY DIFFRACTION	f_chiral_restr	0.042	1204
X-RAY DIFFRACTION	f_plane_restr	0.003	1294

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 (%)
2.4619-2.4899	0.3946	146	0.4177	2435	X-RAY DIFFRACTION	96
2.4899-2.5191	0.4415	178	0.3728	2456	X-RAY DIFFRACTION	100
2.5191-2.5499	0.4779	140	0.3951	2593	X-RAY DIFFRACTION	100
2.5499-2.5821	0.3733	138	0.3845	2469	X-RAY DIFFRACTION	100
2.5821-2.6161	0.4391	136	0.3618	2461	X-RAY DIFFRACTION	100
2.6161-2.6519	0.3775	128	0.326	2557	X-RAY DIFFRACTION	100
2.6519-2.6898	0.3221	112	0.3088	2499	X-RAY DIFFRACTION	100
2.6898-2.73	0.3255	172	0.3045	2505	X-RAY DIFFRACTION	100
2.73-2.7726	0.3868	136	0.3065	2488	X-RAY DIFFRACTION	100
2.7726-2.8181	0.3075	136	0.2991	2512	X-RAY DIFFRACTION	100
2.8181-2.8667	0.3016	115	0.3001	2509	X-RAY DIFFRACTION	100
2.8667-2.9188	0.3361	148	0.2947	2556	X-RAY DIFFRACTION	100
2.9188-2.9749	0.3125	126	0.2852	2497	X-RAY DIFFRACTION	100
2.9749-3.0356	0.2957	110	0.2728	2508	X-RAY DIFFRACTION	100
3.0356-3.1016	0.2848	154	0.2736	2494	X-RAY DIFFRACTION	100
3.1016-3.1738	0.2574	142	0.2529	2549	X-RAY DIFFRACTION	100
3.1738-3.2531	0.292	128	0.2558	2479	X-RAY DIFFRACTION	100
3.2531-3.341	0.2765	138	0.2443	2589	X-RAY DIFFRACTION	100
3.341-3.4393	0.2625	138	0.2353	2463	X-RAY DIFFRACTION	100
3.4393-3.5503	0.2109	151	0.2248	2498	X-RAY DIFFRACTION	100
3.5503-3.6771	0.2315	116	0.2441	2501	X-RAY DIFFRACTION	99
3.6771-3.8243	0.2788	124	0.224	2465	X-RAY DIFFRACTION	98
3.8243-3.9983	0.2902	111	0.1919	2551	X-RAY DIFFRACTION	99
3.9983-4.2089	0.1639	111	0.1799	2483	X-RAY DIFFRACTION	100
4.2089-4.4724	0.1769	150	0.1528	2521	X-RAY DIFFRACTION	100
4.4724-4.8174	0.1952	160	0.1508	2497	X-RAY DIFFRACTION	100
4.8174-5.3016	0.1814	156	0.1592	2504	X-RAY DIFFRACTION	100
5.3016-6.0674	0.2489	154	0.1794	2477	X-RAY DIFFRACTION	100
6.0674-7.6389	0.1857	177	0.1995	2452	X-RAY DIFFRACTION	100
7.6389-46.7722	0.224	119	0.1853	2549	X-RAY DIFFRACTION	100

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	1.6296	-1.047	0.996	2.7926	-0.6708	0.5793	-0.1848	-0.5378	-0.2765	0.4415	0.0389	0.3253	0.1845	-0.1817	-0.007	0.7296	0.0476	0.1955	0.7504	-0.054	0.5905	-22.1889	-7.9094	30.6055
2	3.1985	-0.3146	1.7489	0.8674	-0.7092	1.833	-0.0137	0.0677	0.1939	-0.0664	0.0618	0.086	0.079	-0.185	-0.0013	0.6331	0.0778	-0.0346	0.7887	-0.1347	0.8361	-53.7098	12.3278	3.3151
3	4.3742	0.0304	1.2238	4.0512	0.3225	1.5974	0.0479	-0.1926	0.8511	0.0415	-0.2524	0.2176	-0.0608	-0.0541	-0.0007	0.5452	0.0063	0.0463	0.6546	-0.2042	0.6025	-26.9005	16.5285	23.6698
4	2.8911	-0.3366	0.3167	1.127	0.0473	2.5813	-0.0412	0.3871	0.0506	-0.3606	-0.2733	0.0059	-0.2076	0.0941	-0.004	0.8702	0.052	-0.0003	0.7096	-0.1288	0.7387	-22.4375	-0.7821	13.2178
5	2.8988	1.3579	-0.8317	3.3166	-0.7296	0.9867	-0.0423	0.0597	-0.1441	-0.0314	-0.1464	0.3663	-0.1784	-0.0715	-0.0064	0.5207	-0.022	-0.0964	0.6163	-0.1759	0.4668	-27.164	-0.3577	-32.2221
6	2.865	0.3876	-1.1926	3.0221	-0.8314	2.187	-0.0457	0.0648	-0.1808	0.0491	0.1635	-0.0088	-0.0001	-0.4275	0.0001	0.6069	-0.0452	0.0344	0.8168	-0.1291	0.8042	-59.3666	-11.4204	-11.4102
7	4.1538	0.1861	-1.0311	3.7594	0.0905	1.4114	0.0453	0.193	-0.7696	-0.0102	-0.2141	0.2435	0.0981	-0.0867	-0.0006	0.5513	-0.008	-0.0315	0.6448	-0.2207	0.575	-26.8771	-16.5636	-33.349
8	2.9512	0.839	-1.1918	1.751	0.9925	2.2232	0.2237	-0.4779	-0.3101	0.4186	-0.4132	0.2216	0.1211	0.1966	-0	0.7646	-0.1236	0.0129	0.7377	-0.1134	0.7093	-26.3578	-2.213	-21.4005
9	0.3141	-0.3377	-0.1729	0.755	-0.0354	0.3728	-0.3411	-0.2193	0.6361	0.7411	-0.1568	-0.6373	0.1805	0.5343	-0.0232	1.1523	-0.0923	-0.1663	0.9678	-0.107	0.7753	-12.8785	8.6146	-28.5076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 73 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 74 through 249 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 250 through 389 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 390 through 522 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 115 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 116 through 249 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 250 through 389 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 390 through 491 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 492 through 522 )

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