PDB-4xti: Structure of IMP dehydrogenase of Ashbya gossypii with IMP bound ...

ID or keywords:

Entry

Database: PDB / ID: 4xti

Title

Structure of IMP dehydrogenase of Ashbya gossypii with IMP bound to the active site

Components

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

Keywords

OXIDOREDUCTASE / IMP dehydrogenase / IMP

Function / homology

Function and homology information

IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Ashbya gossypii ATCC 10895 (fungus)

Ashbya gossypii (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Buey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L.

Citation

Journal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Increased riboflavin production by manipulation of inosine 5'-monophosphate dehydrogenase in Ashbya gossypii.
Authors: Buey, R.M. / Ledesma-Amaro, R. / Balsera, M. / de Pereda, J.M. / Revuelta, J.L.

History

Deposition	Jan 23, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 22, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	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 / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_symmetry / _struct_conn_type.id
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xti.cif.gz	401.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4xti.ent.gz	332.1 KB	Display	PDB format
PDBx/mmJSON format	4xti.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4xti_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4xti_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4xti_validation.xml.gz	30.1 KB	Display
Data in CIF	4xti_validation.cif.gz	44.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xt/4xti ftp://data.pdbj.org/pub/pdb/validation_reports/xt/4xti	HTTPS FTP

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Related structure data

Related structure data	4xtdC 4xwuC 4avfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xtd-2 4z0g-1 4my9-1 4my1-2 1jr1-2 5uuz-2 4fo4-2 4xtd-1 4z0g-2 5urr-1 Search similar-shape structures by Omokage search (details) 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)

Deposited unit

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

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

1

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

A: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by author&software
180 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

B: Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

hetero molecules

defined by author&software
180 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	117.775, 117.775, 56.728
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	75
Space group name H-M	P4

#1: Protein	Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase / IMPDH / IMP dehydrogenase / IMPDH / IMP dehydrogenase / IMPDH Mass: 44528.555 Da / Num. of mol.: 2 / Fragment: UNP residues 11-119,UNP residues 236-522 Mutation: The whole CBS domain (residuoes 120-235) has been replaced by the sequence stretch SQDG. All residues numbered according to the full-length wild type protein. Source method: isolated from a genetically manipulated source Details: IMP bound to the active site Source: (gene. exp.) Ashbya gossypii ATCC 10895 (fungus), (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus) Gene: AGOS_AER117W / Production host: Escherichia coli (E. coli) / References: UniProt: Q756Z6, IMP dehydrogenase
#2: Chemical	ChemComp-IMP / INOSINIC ACID Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 25% (v/v) 1,2 propanediol, 0.1 M phosphate-citrate pH 4.2, 5% (w/v) PEG-3000, 10% (v/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 1.5→46.88 Å / Num. obs: 124507 / % possible obs: 100 % / Redundancy: 12.6 % / R_merge(I) obs: 0.0898 / Net I/σ(I): 15.15
Reflection shell	Resolution: 1.5→1.54 Å / Redundancy: 11.75 % / R_merge(I) obs: 1.467 / Mean I/σ(I) obs: 1.43 / CC_1/2: 0.655 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1839)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4AVF

4avf

Resolution: 1.5→46.884 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.03 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.1778	6129	4.92 %
R_work	0.1558	-	-
obs	0.1614	124497	100 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→46.884 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5425	0	48	415	5888

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5569
X-RAY DIFFRACTION	f_angle_d	0.641	7547
X-RAY DIFFRACTION	f_dihedral_angle_d	10.548	1923
X-RAY DIFFRACTION	f_chiral_restr	0.023	892
X-RAY DIFFRACTION	f_plane_restr	0.003	960

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 (%)
1.5004-1.5262	0.3151	323	0.2968	5842	X-RAY DIFFRACTION	95
1.5262-1.554	0.2854	308	0.2675	5859	X-RAY DIFFRACTION	95
1.554-1.5839	0.2602	333	0.2615	5851	X-RAY DIFFRACTION	95
1.5839-1.6162	0.266	282	0.2534	5961	X-RAY DIFFRACTION	95
1.6162-1.6513	0.2305	287	0.2305	5873	X-RAY DIFFRACTION	95
1.6513-1.6897	0.2132	283	0.2244	5884	X-RAY DIFFRACTION	95
1.6897-1.732	0.2323	302	0.2199	5892	X-RAY DIFFRACTION	95
1.732-1.7788	0.2047	300	0.2038	5909	X-RAY DIFFRACTION	95
1.7788-1.8311	0.223	291	0.2	5929	X-RAY DIFFRACTION	95
1.8311-1.8902	0.2208	279	0.2029	5911	X-RAY DIFFRACTION	95
1.8902-1.9578	0.1857	294	0.1976	5907	X-RAY DIFFRACTION	95
1.9578-2.0361	0.2058	323	0.1881	5887	X-RAY DIFFRACTION	95
2.0361-2.1288	0.2004	322	0.1814	5851	X-RAY DIFFRACTION	95
2.1288-2.241	0.1703	334	0.1737	5891	X-RAY DIFFRACTION	95
2.241-2.3813	0.1752	337	0.1658	5901	X-RAY DIFFRACTION	95
2.3813-2.5651	0.1785	339	0.1577	5901	X-RAY DIFFRACTION	95
2.5651-2.823	0.1521	273	0.1529	5966	X-RAY DIFFRACTION	96
2.823-3.231	0.1814	268	0.1457	5979	X-RAY DIFFRACTION	96
3.231-4.0688	0.1537	302	0.1252	6007	X-RAY DIFFRACTION	95
4.0688-28.3124	0.167	349	0.1274	6074	X-RAY DIFFRACTION	95

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	0.3439	0.2144	-0.101	0.2104	0.0474	0.1969	-0.1299	-0.218	0.1127	0.3456	0.0934	-0.0628	-0.0604	0.0397	0.0001	0.2894	0.0169	-0.0199	0.2783	-0.0106	0.1719	57.3587	154.9576	-13.1981
2	0.5262	0.0226	0.0863	0.4782	0.0469	0.3463	-0.0179	0.0864	-0.0582	-0.0851	0.0243	0.0653	-0.0216	-0.0453	0	0.1878	-0.0097	-0.0038	0.201	-0.0015	0.1599	29.489	160.4133	-35.3336
3	0.2286	0.0953	0.0321	0.0713	-0.0903	0.3442	-0.0456	0.0503	0.0191	-0.0452	0.0447	0.1691	0.0044	-0.0961	0.0001	0.2203	-0.0063	-0.0306	0.2485	-0.0027	0.2453	15.6429	164.5315	-36.1551
4	0.0552	0.0147	-0.0028	0.0352	0.0632	0.132	0.0222	0.0447	0.0322	0.0027	-0.0481	0.2385	-0.0163	-0.1448	-0	0.2012	0.0148	0.0012	0.2242	-0.0103	0.233	18.755	174.873	-27.7206
5	0.6726	-0.2506	0.0704	0.8431	0.1382	0.5165	-0.0064	-0.0456	-0.0235	0.0281	0.0044	0.0308	-0.032	0.0156	0	0.1776	-0.0037	-0.0029	0.1685	0.0013	0.1466	33.2693	170.6144	-26.0979
6	0.1884	0.1897	-0.0508	0.1913	-0.0606	0.2584	-0.0398	0.2244	0.0069	-0.1727	-0.0018	-0.0001	-0.0347	-0.0113	0	0.2749	-0.0209	-0.0123	0.303	0.0018	0.2126	34.3628	172.0526	-49.0121
7	0.2912	0.0637	-0.0629	0.1852	0.0002	0.0701	0.006	-0.0664	0.0117	0.0232	0.0046	0.0388	-0.0768	-0.0078	-0	0.2068	0.0028	-0.0047	0.2051	-0.0032	0.1643	40.2903	152.66	-28.9041
8	0.183	-0.0446	-0.0225	0.1344	0.0833	0.0517	0.0855	0.1192	0.0713	-0.0591	-0.0056	0.0288	-0.0747	-0.1363	-0	0.2417	0.0146	-0.012	0.2522	0.0261	0.2331	55.7135	161.7462	-34.4113
9	0.9005	-0.43	-0.0406	0.5545	-0.0135	0.1995	-0.0142	0.0319	0.1003	0.0236	0.0151	-0.0706	-0.0052	0.0001	0	0.2043	-0.0129	-0.0168	0.1869	0.0008	0.1529	7.8016	144.2428	-16.1975
10	0.1988	-0.2106	-0.121	0.2947	-0.0166	0.366	0.0075	0.0253	0.1742	0.0398	0.0231	-0.0033	-0.1462	0.0074	-0	0.2493	0.0233	-0.017	0.2199	-0.03	0.237	-8.6154	161.8485	-9.1246
11	0.1271	-0.0404	-0.1145	0.1302	0.0573	0.1069	-0.039	0.0699	0.1224	0.0029	0.0664	-0.0895	-0.0658	-0.0293	-0	0.2019	0.0162	-0.0235	0.1919	0.0023	0.2046	-14.8536	155.3155	-17.6552
12	0.9331	-0.0031	-0.0164	0.5985	0.2632	0.6643	-0.0188	0.0097	0.0327	-0.0348	0.0103	-0.0487	0.0193	-0.0425	0	0.1759	0.0003	-0.0041	0.1713	0.0009	0.1401	-4.9696	143.5972	-18.9458
13	0.0971	0.0094	-0.07	0.2832	-0.0405	0.1672	-0.0558	-0.2348	0.0007	0.1715	0.0477	0.0081	-0.014	-0.0573	0.0001	0.304	0.0129	-0.0096	0.2999	-0.0004	0.2089	-5.6288	142.3381	3.9173
14	0.0522	-0.0456	0.0265	0.0411	-0.0178	0.037	-0.0519	-0.1621	0.0064	0.1441	0.0615	-0.0353	0.0512	0.132	-0	0.231	0.0003	-0.0166	0.2266	-0.0188	0.2244	14.7738	144.7154	-9.4414
15	0.3879	-0.2057	0.0827	0.4043	0.1667	0.1676	-0.0162	-0.0742	-0.0171	0.0611	0.0005	0.0144	0.0228	0.0023	0.0001	0.2231	-0.0095	-0.0076	0.2435	0.0003	0.2234	12.6608	132.8296	-15.6836

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 114 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 115 through 268 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 269 through 296 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 297 through 389 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 390 through 459 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 460 through 492 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 493 through 521 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 114 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 115 through 268 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 269 through 296 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 297 through 389 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 390 through 459 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 460 through 478 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 479 through 521 )

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