PDB-5m2e: Apo structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, ICD.

ID or keywords:

Entry

Database: PDB / ID: 5m2e

Title

Apo structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, ICD.

Components

Isocitrate dehydrogenase [NADP]

Keywords

OXIDOREDUCTASE / Isocitrate Dehydrogenase / Pseudomonas aeruginosa / Metabolism

Function / homology

Function and homology information

isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding / extracellular region
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Crousilles, A. / Welch, M.

Funding support

United Kingdom, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Gluconeogenic precursor availability regulates flux through the glyoxylate shunt inPseudomonas aeruginosa.
Authors: Crousilles, A. / Dolan, S.K. / Brear, P. / Chirgadze, D.Y. / Welch, M.

History

Deposition	Oct 12, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.pdb_format_compatible
Revision 1.2	Sep 26, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.4	Feb 7, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5m2e.cif.gz	921.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5m2e.ent.gz		Display	PDB format
PDBx/mmJSON format	5m2e.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5m2e_validation.pdf.gz	460.9 KB	Display	wwPDB validaton report
Full document	5m2e_full_validation.pdf.gz	488.5 KB	Display
Data in XML	5m2e_validation.xml.gz	56.3 KB	Display
Data in CIF	5m2e_validation.cif.gz	75.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m2/5m2e ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m2e	HTTPS FTP

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Related structure data

Related structure data	6g1oC 6g3uC 1bl5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3b46-d 4ba4-d 3bui-d 3cv5-d 3bvx-d 1mdp-d 5uts-1 1sjs-1 5v1x-3 5v12-4 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (5)

Deposited unit

A: Isocitrate dehydrogenase [NADP]

B: Isocitrate dehydrogenase [NADP]

C: Isocitrate dehydrogenase [NADP]

D: Isocitrate dehydrogenase [NADP]

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

1

A: Isocitrate dehydrogenase [NADP]

B: Isocitrate dehydrogenase [NADP]

defined by author&software
91.3 kDa, 2 polymers

2

C: Isocitrate dehydrogenase [NADP]

D: Isocitrate dehydrogenase [NADP]

defined by author&software
91.3 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	88.884, 95.554, 104.015
Angle α, β, γ (deg.)	90.00, 99.19, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Isocitrate dehydrogenase [NADP] / IDH / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase Mass: 45626.223 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: icd, PA14_30190 / Plasmid: pQE80 / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: Q02NB5, isocitrate dehydrogenase (NADP+)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Isocitrate dehydrogenase [NADP] / IDH / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase

Mass: 45626.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria) / Gene: icd, PA14_30190 / Plasmid: pQE80 / Production host:

Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q02NB5, isocitrate dehydrogenase (NADP+)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.39 Å³/Da / Density % sol: 48.52 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1M Sodium acetate, 30% PEG300

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Data collection

Diffraction	Mean temperature: 294 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9174 Å / Relative weight: 1
Reflection	Resolution: 2.68→52 Å / Num. obs: 46653 / % possible obs: 98.4 % / Redundancy: 6.9 % / Net I/σ(I): 16.2

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Processing

Software

Name	Version	Classification
PHENIX	1.10-2155	refinement
Coot	0.8.1	model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BL5

1bl5

Resolution: 2.7→47.777 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 32.42

	R_factor	Num. reflection	% reflection
R_free	0.2836	1998	4.28 %
R_work	0.2454	-	-
obs	0.247	46646	98.46 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→47.777 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12796	0	0	36	12832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13040
X-RAY DIFFRACTION	f_angle_d	0.598	17660
X-RAY DIFFRACTION	f_dihedral_angle_d	14.394	7876
X-RAY DIFFRACTION	f_chiral_restr	0.044	1984
X-RAY DIFFRACTION	f_plane_restr	0.004	2284

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 (%)
2.7-2.7675	0.42	140	0.3486	3143	X-RAY DIFFRACTION	97
2.7675-2.8423	0.4236	137	0.3356	3049	X-RAY DIFFRACTION	96
2.8423-2.926	0.3488	144	0.3199	3210	X-RAY DIFFRACTION	99
2.926-3.0204	0.3383	143	0.2972	3189	X-RAY DIFFRACTION	100
3.0204-3.1283	0.352	144	0.303	3224	X-RAY DIFFRACTION	100
3.1283-3.2536	0.3024	144	0.2744	3213	X-RAY DIFFRACTION	100
3.2536-3.4016	0.2857	144	0.2656	3205	X-RAY DIFFRACTION	100
3.4016-3.5809	0.2961	144	0.2664	3223	X-RAY DIFFRACTION	99
3.5809-3.8051	0.3082	143	0.2464	3198	X-RAY DIFFRACTION	99
3.8051-4.0988	0.3002	140	0.2392	3114	X-RAY DIFFRACTION	97
4.0988-4.511	0.2719	142	0.2106	3175	X-RAY DIFFRACTION	98
4.511-5.1631	0.2344	145	0.2003	3217	X-RAY DIFFRACTION	99
5.1631-6.5023	0.2548	145	0.253	3256	X-RAY DIFFRACTION	99
6.5023-47.7845	0.2514	143	0.2242	3232	X-RAY DIFFRACTION	97

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	0.0343	-0.0003	-0.026	0.0066	0.0059	0.0359	0.0902	-0.1121	-0.1896	0.0081	0.088	-0.0079	-0.1936	0.0999	0.0001	0.6809	0.1343	-0.0301	0.834	0.1315	0.6407	93.7621	20.7502	64.6303
2	0.0681	0.0032	0.0164	0.0167	0.0036	0.0347	0.094	-0.2355	-0.1025	0.1223	-0.1227	-0.3542	0.1483	0.0167	-0	0.5278	0.0718	0.0463	0.4669	0.1449	0.4401	89.6792	31.2077	66.2394
3	1.1475	-0.1888	-0.2756	0.4935	0.3458	0.2534	-0.0251	-0.1334	-0.1135	-0.1005	0.0008	0.0161	-0.0222	0.0857	-0.0059	0.4601	-0.0138	0.0512	0.1848	0.0066	0.2445	69.8271	26.7772	56.8448
4	0.0124	-0.0256	0.0453	0.0175	-0.0308	0.0565	0.1376	0.2198	0.0788	0.0115	0.1396	0.4356	-0.3092	-0.2945	0.0009	0.8057	0.2476	-0.1437	0.9615	-0.0999	0.9441	30.6601	43.7748	36.4646
5	0.008	0.0007	-0.0136	0.0078	-0.0057	0.0129	-0.0747	0.0715	0.0204	-0.06	-0.0819	0.0897	-0.0151	-0.0971	-0	0.8213	0.1387	0.0337	0.8724	-0.1417	0.5909	41.3123	38.4664	32.3622
6	0.5522	-0.1893	0.4484	0.3879	-0.2846	0.5267	0.1753	0.0206	0.19	-0.1314	-0.2095	0.0283	-0.1703	-0.2653	0.0017	0.6547	0.0435	0.0396	0.3222	-0.0518	0.429	51.7621	41.8934	48.8537
7	0.0303	0.0488	0.0339	0.0657	0.0443	0.0235	0.0663	-0.2681	0.2913	0.0813	0.1292	-0.1415	-0.1785	0.1277	0.2313	0.398	-0.1935	0.0107	1.6879	-0.7874	0.8688	79.9259	63.52	103.6998
8	0.3194	0.1121	-0.2396	0.0656	-0.0811	0.1761	0.2811	-0.1231	0.0163	0.0777	0.1293	-0.052	-0.017	-0.0574	0.0464	0.6859	0.0431	-0.1083	1.5597	-0.3783	0.5928	75.3135	53.4579	113.2752
9	0.1045	-0.0664	-0.0269	0.0749	-0.0605	0.1792	0.1364	-0.1254	0.2419	-0.1294	0.1046	-0.0893	0.0221	0.0381	0.0415	0.471	-0.1845	0.1149	1.2314	-0.481	0.5981	63.023	54.6484	107.6195
10	0.2668	-0.2581	0.0884	0.3914	-0.2416	0.4919	0.0891	-0.6212	0.5759	-0.0701	0.5847	-0.0228	-0.206	0.1545	0.2861	0.4397	-0.1065	0.1912	0.5816	-0.2211	0.5451	46.4383	62.1569	106.3479
11	0.12	-0.0238	0.1683	0.0407	-0.0781	0.2699	0.1228	-0.0412	-0.1502	-0.0937	0.1627	0.1661	0.1631	-0.0536	0.0639	0.752	0.0684	0.4423	0.1626	0.1392	0.6586	47.7011	77.5998	96.5121
12	0.3851	-0.167	-0.0583	0.103	-0.1025	0.2945	0.3202	-0.4577	0.344	-0.1654	0.4254	-0.3167	0.0393	0.7374	1.388	0.0107	-0.6287	-0.1703	0.5977	-0.6929	0.3254	66.4418	59.4727	90.8695
13	0.0558	0.035	-0.1268	0.0235	-0.0743	0.2568	-0.1305	0.0306	-0.0672	-0.1205	-0.2109	0.0337	0.1073	-0.1326	-0.0356	0.4848	-0.1597	-0.3029	0.916	0.1223	1.2369	9.7497	46.4694	89.4277
14	0.0051	-0.0478	-0.0376	0.1851	0.0512	0.1485	0.3612	-0.0539	-0.3607	-0.3905	-0.0125	0.3918	0.0445	-0.1602	0.0305	0.5238	-0.0334	-0.181	0.8852	0.1218	0.9689	14.0169	57.1944	89.1541
15	0.1436	-0.2402	-0.1064	0.8153	-0.103	0.1788	0.0302	-0.2451	0.0076	-0.0412	0.0893	0.5236	0.0221	-0.2918	0.0482	0.3081	-0.023	0.014	0.8325	0.0732	0.5939	36.4543	52.6591	103.1163
16	0.2108	-0.1152	-0.146	0.2377	0.2563	0.3264	-0.0575	-0.0038	-0.2515	-0.2363	0.1116	0.3037	0.1331	-0.3468	-0.2594	0.4789	-0.0344	-0.1808	0.4673	0.1225	0.5419	34.6448	49.0508	86.4305

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 116 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 117 through 418 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 87 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 88 through 115 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 116 through 418 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 74 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 75 through 102 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 103 through 134 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 135 through 253 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 254 through 293 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 294 through 418 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 37 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 38 through 116 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 117 through 221 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 222 through 418 )

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