PDB-5uxe: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from ...

ID or keywords:

Entry

Database: PDB / ID: 5uxe

Title

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P178

Components

Inosine-5'-monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR /

TIM barrel / IMPDH / CSGID /

dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

IMP dehydrogenase activity /

IMP dehydrogenase / GMP biosynthetic process /

nucleotide binding /

metal ion binding
Similarity search - Function

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Maltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and P178
Authors: Maltseva, N. / Kim, Y. / Mulligan, R. / Makowska-Grzyska, M. / Gu, M. / Gollapalli, D.R. / Hedstrom, L. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Feb 22, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uxe.cif.gz	535.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5uxe.ent.gz	440.1 KB	Display	PDB format
PDBx/mmJSON format	5uxe.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/ux/5uxe ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5uxe	HTTPS FTP

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Related structure data

Related structure data	4q32S 4q33 5uwx S: Starting model for refinement
Similar structure data	4q33-2 5uze-d 5uzc-d 5uuv-d 5vsv-d 4my9-1 4mya-2 5urr-2 4x3z-2 2cu0-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP04376

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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)

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

C: Inosine-5'-monophosphate dehydrogenase

D: Inosine-5'-monophosphate dehydrogenase

hetero molecules

158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	127.937, 119.101, 96.971
Angle α, β, γ (deg.)	90.00, 102.86, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Inosine-5'-monophosphate dehydrogenase / IMPDH Mass: 38441.266 Da / Num. of mol.: 4 Mutation: CBS domain (residues 89-215) is replaced with SGG residues Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: guaB_2, guaB, ERS852446_02285, JFP838_13815 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A127ELD1, IMP dehydrogenase

#1: Protein

Inosine-5'-monophosphate dehydrogenase / IMPDH

Mass: 38441.266 Da / Num. of mol.: 4
Mutation: CBS domain (residues 89-215) is replaced with SGG residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium perfringens (bacteria) / Gene: guaB_2, guaB, ERS852446_02285, JFP838_13815 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A127ELD1,

IMP dehydrogenase

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Non-polymers , 7 types, 247 molecules

#2: Chemical	ChemComp-IMP / INOSINIC ACID / Inosinic acid Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#3: Chemical	ChemComp-8LA / N-[4-chloro-3-(alpha-D-ribofuranosyloxy)phenyl]-N'-{2-[3-(prop-1-en-2-yl)phenyl]propan-2-yl}urea Mass: 476.950 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₄H₂₉ClN₂O₆
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#6: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#7: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.48 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M ammonium acetate, 0.1M Bis-Tris pH 6.5, 45% MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2015 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 80071 / % possible obs: 94.4 % / Redundancy: 2.7 % / R_sym value: 0.086 / Net I/σ(I): 11.14
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 2.2 % / Num. unique obs: 3680 / CC_1/2: 0.625 / R_sym value: 0.614 / % possible all: 88.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Q32

4q32

Resolution: 2.1→39.253 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.74

	R_factor	Num. reflection	% reflection
R_free	0.2233	3908	4.89 %
R_work	0.1732	-	-
obs	0.1757	79873	92.6 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→39.253 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10115	0	251	232	10598

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10694
X-RAY DIFFRACTION	f_angle_d	0.919	14490
X-RAY DIFFRACTION	f_dihedral_angle_d	8.072	8765
X-RAY DIFFRACTION	f_chiral_restr	0.055	1677
X-RAY DIFFRACTION	f_plane_restr	0.005	1851

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 (%)
2.069-2.0943	0.3469	76	0.2953	1322	X-RAY DIFFRACTION	46
2.0943-2.1208	0.3146	121	0.2505	2579	X-RAY DIFFRACTION	89
2.1208-2.1487	0.2893	134	0.2359	2597	X-RAY DIFFRACTION	89
2.1487-2.1781	0.2747	145	0.2254	2606	X-RAY DIFFRACTION	90
2.1781-2.2092	0.2744	125	0.2331	2663	X-RAY DIFFRACTION	89
2.2092-2.2422	0.3184	131	0.2185	2625	X-RAY DIFFRACTION	90
2.2422-2.2772	0.2776	126	0.218	2649	X-RAY DIFFRACTION	91
2.2772-2.3146	0.27	135	0.2114	2690	X-RAY DIFFRACTION	91
2.3146-2.3545	0.2464	121	0.2116	2682	X-RAY DIFFRACTION	92
2.3545-2.3973	0.2642	147	0.2004	2703	X-RAY DIFFRACTION	92
2.3973-2.4434	0.2515	135	0.1981	2687	X-RAY DIFFRACTION	93
2.4434-2.4932	0.2479	161	0.1955	2773	X-RAY DIFFRACTION	94
2.4932-2.5474	0.2499	179	0.1886	2682	X-RAY DIFFRACTION	94
2.5474-2.6067	0.2451	136	0.1943	2773	X-RAY DIFFRACTION	94
2.6067-2.6719	0.2342	134	0.1853	2736	X-RAY DIFFRACTION	94
2.6719-2.7441	0.2488	131	0.1964	2784	X-RAY DIFFRACTION	94
2.7441-2.8248	0.2777	152	0.1893	2769	X-RAY DIFFRACTION	95
2.8248-2.916	0.2538	126	0.1947	2817	X-RAY DIFFRACTION	95
2.916-3.0201	0.2655	138	0.1935	2750	X-RAY DIFFRACTION	95
3.0201-3.141	0.2347	153	0.1873	2817	X-RAY DIFFRACTION	96
3.141-3.2839	0.2385	152	0.1819	2772	X-RAY DIFFRACTION	96
3.2839-3.4569	0.2104	143	0.1666	2871	X-RAY DIFFRACTION	97
3.4569-3.6734	0.2177	155	0.1608	2848	X-RAY DIFFRACTION	98
3.6734-3.9568	0.2147	146	0.1513	2948	X-RAY DIFFRACTION	100
3.9568-4.3545	0.1862	154	0.1339	2920	X-RAY DIFFRACTION	100
4.3545-4.9835	0.1555	169	0.1354	2938	X-RAY DIFFRACTION	100
4.9835-6.2745	0.2019	142	0.1649	2964	X-RAY DIFFRACTION	100
6.2745-39.26	0.1931	141	0.1479	3000	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	0.9584	-0.2405	-0.4828	1.9144	0.4344	1.265	0.1534	-0.282	0.4582	0.1489	-0.0251	-0.1973	-0.5232	0.2002	-0.1184	0.5071	-0.1662	0.08	0.3679	-0.101	0.4378	11.7715	29.1549	28.0923
2	3.0733	2.5715	1.6016	4.4828	2.1611	1.2502	0.019	0.119	0.5874	-0.2061	0.0294	-0.017	-0.6509	0.1837	-0.0489	0.6388	-0.1179	0.1688	0.3009	-0.0121	0.4551	5.3566	38.7145	16.9002
3	1.9231	-0.4238	0.1515	1.2972	-0.0029	0.8081	0.0197	-0.0639	0.1263	0.0431	0.1444	-0.1434	-0.319	0.1629	-0.147	0.3448	-0.098	0.0641	0.2257	-0.066	0.2885	5.4364	21.9645	27.1901
4	2.0042	-0.8505	-1.0122	2.2331	1.3707	1.4468	0.1356	-0.1111	0.2167	-0.0334	-0.0074	-0.2852	-0.275	0.1786	-0.1207	0.3271	-0.1003	0.0128	0.2637	-0.0066	0.2336	9.5905	17.0484	29.6643
5	2.1098	0.4374	0.6909	3.8049	1.1379	4.661	-0.1885	-0.4349	0.2721	0.4084	0.1062	0.3352	-0.1812	-0.3183	-0.0188	0.3037	-0.0962	0.0292	0.4288	-0.0758	0.3614	9.9867	3.7062	40.8305
6	2.4389	2.6151	-0.1941	2.7646	0.0632	0.6387	-0.0166	0.0314	-0.068	-0.0887	0.1147	-0.311	-0.0333	0.1119	-0.0296	0.1623	0.0043	0.0103	0.2631	-0.0108	0.2193	10.5593	-9.9804	16.6826
7	1.8095	0.5556	0.5358	2.1345	0.9331	1.9262	0.2627	-0.498	-0.3316	0.3964	-0.2042	-0.5029	0.0694	0.0839	-0.0699	0.3095	-0.015	-0.1154	0.4382	0.1339	0.361	25.8795	-17.9041	35.8057
8	4.3789	-0.5745	2.1527	8.8625	-0.1873	7.0438	0.0235	-1.0279	-0.2301	0.801	0.1729	-0.4275	0.2033	0.408	-0.1777	0.2791	-0.0354	-0.0992	0.6947	0.0648	0.396	36.4288	-11.6564	43.1322
9	0.6584	-1.2679	1.1004	3.0604	-1.6177	2.2313	-0.0827	-0.2738	0.2282	0.2413	-0.0777	-0.5819	-0.1701	0.4517	0.1518	0.216	-0.0727	-0.0577	0.5627	0.0352	0.4556	37.1822	-6.3903	34.8664
10	3.6195	-1.5898	3.1896	5.081	-1.8436	4.0358	-0.0097	-0.064	0.1192	0.0926	-0.1456	-0.6248	-0.194	0.4519	0.1513	0.1861	-0.0556	0.0337	0.4031	0.0112	0.3387	36.4641	-4.5787	24.396
11	1.6696	0.3313	-0.2119	1.9759	0.3858	0.8204	0.1992	-0.3417	-0.0287	0.193	-0.1031	-0.0348	0.0336	0.1869	-0.075	0.1703	-0.0415	-0.0228	0.3378	0.0042	0.1936	17.6599	-8.6684	32.0316
12	1.9033	0.149	0.5896	2.1483	0.9035	2.232	0.1134	-0.2213	-0.2268	0.1851	0.0393	-0.1932	-0.0051	0.2066	-0.1725	0.1533	-0.0505	0.021	0.2831	0.0659	0.2177	13.04	-13.8021	30.9336
13	7.2659	-1.5403	-0.5305	5.3093	-2.1777	6.8458	0.1207	-0.6175	0.4478	0.5551	-0.1139	-0.0948	-0.3607	-0.2404	-0.0106	0.2833	0.0048	0.0256	0.3187	-0.0111	0.3604	-3.1932	-17.33	36.9073
14	2.9526	-0.0891	-0.1349	0.9298	-0.0707	0.9849	0.0646	0.1772	-0.112	-0.1578	-0.0273	0.3608	-0.1875	-0.2232	-0.0368	0.3271	0.1148	-0.0006	0.2847	-0.006	0.3113	-31.7755	14.196	13.2371
15	4.6786	-4.0756	0.0066	4.7722	-0.4046	0.3877	0.0405	0.0804	-0.3798	0.0652	0.0744	0.4956	-0.0008	-0.2346	-0.1228	0.3224	0.1178	-0.0879	0.3901	-0.0605	0.3695	-37.6076	4.6688	3.5977
16	2.4099	-0.4309	0.5572	2.3903	-0.4369	1.7658	0.1203	0.4035	-0.0643	-0.3906	-0.098	0.0913	-0.1326	-0.1131	-0.0473	0.2516	0.0894	-0.0119	0.2647	-0.0302	0.2261	-24.4861	4.843	5.6728
17	2.1854	0.1401	-1.2731	2.6027	-0.3878	2.2403	0.1211	-0.175	0.0219	0.102	-0.1065	0.1492	-0.1806	-0.0232	-0.0301	0.2342	0.0424	0.0026	0.2478	-0.0209	0.2664	-25.3909	12.4453	23.2069
18	2.734	0.117	-1.3028	2.6593	-0.5562	2.5434	0.142	-0.1285	-0.0102	0.1687	-0.0875	0.3796	-0.1895	-0.0584	-0.0481	0.1902	0.0635	-0.0008	0.2234	-0.027	0.2695	-25.9003	11.4005	23.9365
19	3.1393	-1.325	-0.0519	3.1751	0.4771	3.1457	0.0273	-0.0604	0.1318	0.0554	-0.0667	0.2106	-0.0922	0.15	0.038	0.2493	-0.087	0.0413	0.1811	-0.014	0.3057	-8.7123	16.9771	20.9971
20	0.4211	-0.4488	-0.4908	2.6563	-0.5313	1.1161	-0.012	0.0279	-0.5363	-0.0271	-0.0774	0.5642	0.2292	-0.0948	0.073	0.2507	-0.0301	0.0186	0.3015	-0.0255	0.683	-16.1984	-30.824	19.3689
21	3.7893	3.1124	-0.3347	4.484	-0.3754	2.297	0.051	0.1769	-0.5618	-0.1726	-0.0519	0.3672	0.299	-0.1438	-0.0048	0.2301	0.0408	-0.0132	0.2707	-0.0591	0.5641	-4.2175	-36.8825	13.5636
22	2.1935	-0.6848	0.073	1.3415	-0.1045	1.7793	-0.0989	-0.1984	-0.3036	0.1181	0.0456	0.426	-0.0124	-0.1256	0.0766	0.1979	-0.0103	0.0426	0.1908	0.003	0.4288	-13.0885	-21.6069	23.7229
23	3.3428	-0.1426	-1.4512	2.6444	0.9855	2.3339	-0.0099	-0.0876	-0.2072	-0.0782	-0.0566	0.2976	-0.0925	0.081	0.0446	0.1922	0.0703	-0.0696	0.1607	0.0228	0.2593	-18.7657	-6.5895	17.8734

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 227 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 228 through 288 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 289 through 384 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 385 through 466 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 467 through 482 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 0 through 24 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 75 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 76 through 227 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 228 through 252 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 253 through 288 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 289 through 384 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 385 through 466 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 467 through 482 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2 through 237 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 238 through 265 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 266 through 329 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 330 through 384 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 385 through 441 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 442 through 482 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 237 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 238 through 287 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 288 through 440 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 441 through 482 )

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