PDB-4xtd: Structure of the covalent intermediate E-XMP* of the IMP dehydrog...

ID or keywords:

Entry

Database: PDB / ID: 4xtd

Title

Structure of the covalent intermediate E-XMP* of the IMP dehydrogenase of Ashbya gossypii

Components

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

Keywords

OXIDOREDUCTASE / XMP

Function / homology

Function and homology information

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

Biological species

Ashbya gossypii (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 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 / 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
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xtd.cif.gz	408.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4xtd.ent.gz	339.3 KB	Display	PDB format
PDBx/mmJSON format	4xtd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4xtd_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	4xtd_full_validation.pdf.gz	1.6 MB	Display
Data in XML	4xtd_validation.xml.gz	28 KB	Display
Data in CIF	4xtd_validation.cif.gz	38.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xt/4xtd ftp://data.pdbj.org/pub/pdb/validation_reports/xt/4xtd	HTTPS FTP

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Related structure data

Related structure data	4xtiC 4xwuC 4avfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z0g-2 4z0g-1 4xti-1 5uqf-2 2cu0-1 4xti-2 4fo4-2 5upu-1 4mz8-2 4ix2-1 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)	117.201, 117.201, 56.095
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 Mass: 44528.555 Da / Num. of mol.: 2 Mutation: The CBS domain (residues 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: The covalent intermediate IMPDH-XMP* bound to Cys334 in the active site and non-covalently bound IMP are present at around 50% in the crystal. Source: (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: isolated from a natural source / Formula: C₁₀H₁₃N₄O₈P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.16 Å³/Da / Density % sol: 43.13 %
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: 0.97926 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: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.05→46.45 Å / Num. obs: 48129 / % possible obs: 100 % / Redundancy: 13.3 % / R_merge(I) obs: 0.1298 / Net I/σ(I): 12.84
Reflection shell	Resolution: 2.05→2.1 Å / Redundancy: 13.2 % / R_merge(I) obs: 2.222 / Mean I/σ(I) obs: 1.23 / CC_1/2: 0.645 / % 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: 2.05→46.454 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2143	2399	4.99 %
R_work	0.1834	-	-
obs	0.1849	48101	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.05→46.454 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5528	0	46	134	5708

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5675
X-RAY DIFFRACTION	f_angle_d	0.668	7698
X-RAY DIFFRACTION	f_dihedral_angle_d	10.95	1959
X-RAY DIFFRACTION	f_chiral_restr	0.025	906
X-RAY DIFFRACTION	f_plane_restr	0.003	983

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 (%)
2.05-2.0919	0.3295	141	0.3151	2671	X-RAY DIFFRACTION	100
2.0919-2.1374	0.2883	137	0.2683	2630	X-RAY DIFFRACTION	100
2.1374-2.1871	0.2725	157	0.2505	2680	X-RAY DIFFRACTION	100
2.1871-2.2418	0.2888	131	0.2498	2693	X-RAY DIFFRACTION	100
2.2418-2.3024	0.2806	154	0.2318	2626	X-RAY DIFFRACTION	100
2.3024-2.3701	0.2774	136	0.2167	2659	X-RAY DIFFRACTION	100
2.3701-2.4466	0.2604	148	0.2071	2696	X-RAY DIFFRACTION	100
2.4466-2.5341	0.2157	130	0.1953	2683	X-RAY DIFFRACTION	100
2.5341-2.6355	0.2651	155	0.1935	2648	X-RAY DIFFRACTION	100
2.6355-2.7555	0.2278	159	0.1908	2657	X-RAY DIFFRACTION	100
2.7555-2.9007	0.2155	130	0.1801	2702	X-RAY DIFFRACTION	100
2.9007-3.0824	0.2251	167	0.1805	2674	X-RAY DIFFRACTION	100
3.0824-3.3204	0.1811	132	0.1745	2697	X-RAY DIFFRACTION	100
3.3204-3.6544	0.1792	124	0.1604	2709	X-RAY DIFFRACTION	100
3.6544-4.1829	0.1717	116	0.1484	2743	X-RAY DIFFRACTION	100
4.1829-5.2688	0.1896	146	0.1537	2723	X-RAY DIFFRACTION	100
5.2688-46.4658	0.2208	136	0.204	2811	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	1.0125	-0.7391	-0.0121	2.5311	0.8952	0.4607	-0.01	-0.0374	0.0554	-0.0393	-0.0021	0.0789	-0.0044	0.0661	-0.0001	0.4262	-0.0229	0.0243	0.4389	0.0356	0.3402	18.8272	135.7968	25.9446
2	0.2319	0.3031	-0.037	2.3303	0.5591	1.7797	0.0146	0.0694	0.4122	0.1699	-0.0654	0.0463	-0.4066	0.0133	0	0.5077	-0.0011	-0.0021	0.4203	-0.0465	0.4807	10.6501	158.9583	35.0828
3	2.2966	-0.4959	0.2124	2.454	0.5098	1.1678	-0.0042	-0.1171	-0.0463	-0.0466	-0.0129	0.1096	-0.0998	-0.1297	-0	0.4145	-0.0042	0.0022	0.4002	0.0038	0.3986	5.3267	145.2019	24.4584
4	0.3369	0.1198	-0.1301	0.4819	-0.1658	0.531	-0.1798	-0.4044	-0.5252	0.3841	0.0312	0.263	-0.1177	-0.4141	-0	0.7214	0.0151	0.0409	0.7616	0.0529	0.626	6.4175	141.9716	49.0245
5	0.4599	-0.4697	0.2377	0.4269	-0.3152	0.4278	-0.1141	-0.1928	-0.3842	0.242	-0.0683	0.1945	0.1219	-0.0822	0	0.4838	-0.0324	-0.0092	0.4843	-0.0334	0.4906	16.5297	137.2681	38.5539
6	0.5864	0.2333	0.2274	1.3549	0.0763	0.3346	-0.096	-0.1676	-0.1986	0.1928	0.0644	0.2198	0.1163	-0.1576	-0	0.56	0.0359	0.0374	0.541	0.0285	0.5589	17.7639	125.6318	27.7585
7	0.9859	-0.141	-0.4173	0.0947	0.0297	1.1003	-0.1526	-0.2837	0.1382	0.5942	0.1201	-0.0529	-0.0482	-0.0723	0.0001	0.5095	0.0305	-0.0413	0.4785	0.0124	0.382	49.2358	158.4518	29.7916
8	1.703	-1.4408	0.7525	1.8331	-0.0682	0.5994	0.1332	0.1637	-0.1402	-0.2042	-0.167	0.1624	0.0639	0.0473	0.0001	0.3804	0.0006	-0.0117	0.4038	-0.007	0.3923	27.1071	170.795	9.5099
9	1.3547	-0.4682	-0.1072	0.8159	-0.2186	0.941	-0.1217	0.2085	0.1386	-0.4697	0.2158	0.7895	-0.1532	-0.497	-0	0.5309	0.0369	-0.1254	0.5719	-0.0341	0.5147	13.8432	178.8708	4.0462
10	1.8292	-0.7128	0.475	2.0486	-0.1776	1.1211	0.0004	-0.0492	0.0052	-0.1052	-0.0346	0.0428	-0.1279	0.0047	-0	0.3812	-0.0013	0.021	0.3647	-0.0127	0.3705	28.5799	183.9821	16.0205
11	0.5759	0.1952	0.1732	0.3857	-0.176	0.5885	0.2015	0.3011	0.1151	-0.6075	-0.3419	-0.2977	-0.5018	0.1946	-0.0003	0.8672	0.0601	0.1265	0.6721	0.0024	0.6495	33.4326	180.4055	-7.1588
12	0.0858	0.1491	-0.0939	0.2254	-0.1517	0.0932	-0.0969	0.3686	0.0074	-0.3608	0.2604	-0.2549	-0.278	0.2118	-0.0002	0.8191	0.0129	-0.11	0.6801	-0.0301	0.6796	36.6038	184.4996	-3.0797
13	1.1174	0.0384	0.4587	1.02	0.6569	0.5909	-0.0591	-0.1142	-0.0831	0.2091	-0.0837	0.0914	0.531	0.3264	-0	0.4106	0.0287	0.0184	0.3914	-0.0377	0.4695	31.7507	161.4607	14.4699
14	0.7122	0.5226	0.4291	0.4058	0.375	0.357	0.0987	0.6581	0.2424	-0.4042	0.1943	-0.5765	-0.1731	0.1733	-0.0001	0.723	0.0386	0.0626	0.7335	0.0149	0.6864	49.8301	163.6491	10.0583

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 102 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 103 through 283 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 284 through 389 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 390 through 424 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 425 through 478 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 479 through 521 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 37 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 38 through 102 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 103 through 256 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 257 through 389 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 390 through 424 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 425 through 459 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 460 through 491 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 492 through 521 )

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