PDB-5j32: Isopropylmalate dehydrogenase in complex with isopropylmalate

ID or keywords:

Entry

Database: PDB / ID: 5j32

Title

Isopropylmalate dehydrogenase in complex with isopropylmalate

Components

3-isopropylmalate dehydrogenase 2, chloroplastic

Keywords

OXIDOREDUCTASE / dehydrogenase / leucine biosynthesis / glucosinolate biosynthesis

Function / homology

Function and homology information

embryo sac development / 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / pollen development / L-leucine biosynthetic process / chloroplast envelope / plastid / chloroplast stroma / NAD+ binding / chloroplast ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.933 Å

Authors

Jez, J.M. / Lee, S.G.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS.
Authors: Lee, S.G. / Nwumeh, R. / Jez, J.M.

History

Deposition	Mar 30, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 11, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 18, 2016	Group: Database references
Revision 1.2	Jul 6, 2016	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_atom_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_atom_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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PDBx/mmCIF format	5j32.cif.gz	583.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5j32.ent.gz	476 KB	Display	PDB format
PDBx/mmJSON format	5j32.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5j32_validation.pdf.gz	474.2 KB	Display	wwPDB validaton report
Full document	5j32_full_validation.pdf.gz	481.5 KB	Display
Data in XML	5j32_validation.xml.gz	65.5 KB	Display
Data in CIF	5j32_validation.cif.gz	98.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j3/5j32 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j32	HTTPS FTP

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Related structure data

Related structure data	5j33C 5j34C 3r8wS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4nas-1 3w5f-2 3w7s-1 4q8h-d 3dtu-1 6gs1-d 3jzf-d 1khk-d 2d69-2 6ik7-2 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 (5) #154 - Oct 2012 Citric Acid Cycle similarity (5)

Deposited unit

A: 3-isopropylmalate dehydrogenase 2, chloroplastic

B: 3-isopropylmalate dehydrogenase 2, chloroplastic

C: 3-isopropylmalate dehydrogenase 2, chloroplastic

D: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

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

1

A: 3-isopropylmalate dehydrogenase 2, chloroplastic

B: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

defined by author&software
86.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 3-isopropylmalate dehydrogenase 2, chloroplastic

D: 3-isopropylmalate dehydrogenase 2, chloroplastic

hetero molecules

defined by author&software
86.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.059, 49.622, 158.969
Angle α, β, γ (deg.)	90.00, 105.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3-isopropylmalate dehydrogenase 2, chloroplastic / IMDH 2 / Beta-IPM dehydrogenase 2 Mass: 43204.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IMDH2, IMDH, At1g80560, T21F11.11 / Production host: Escherichia coli (E. coli) References: UniProt: P93832, 3-isopropylmalate dehydrogenase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical	ChemComp-IPM / 3-ISOPROPYLMALIC ACID Mass: 176.167 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₁₂O₅
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1434 / 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: 2.1 Å³/Da / Density % sol: 41.48 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.0 M ammonium phosphate, 0.1 M imidazole, pH 8.0, and 5 mM isopropylmalate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.93→32.5 Å / Num. obs: 104824 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.15 % / R_sym value: 0.093 / Net I/σ(I): 11
Reflection shell	Resolution: 1.93→1.96 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.624 / Mean I/σ(I) obs: 2 / % possible all: 92.6

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3R8W

3r8w

Resolution: 1.933→32.475 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.198	5246	5.01 %
R_work	0.1587	-	-
obs	0.1607	104735	96.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.933→32.475 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10948	0	52	1434	12434

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11222
X-RAY DIFFRACTION	f_angle_d	1.021	15189
X-RAY DIFFRACTION	f_dihedral_angle_d	13.326	4201
X-RAY DIFFRACTION	f_chiral_restr	0.066	1746
X-RAY DIFFRACTION	f_plane_restr	0.005	1998

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 (%)
1.9328-1.9548	0.2697	177	0.2045	2790	X-RAY DIFFRACTION	83
1.9548-1.9778	0.2526	167	0.1925	3206	X-RAY DIFFRACTION	93
1.9778-2.0019	0.2319	179	0.1923	3324	X-RAY DIFFRACTION	95
2.0019-2.0272	0.2633	161	0.1885	3183	X-RAY DIFFRACTION	95
2.0272-2.0539	0.2294	174	0.1774	3208	X-RAY DIFFRACTION	93
2.0539-2.082	0.2282	203	0.1765	3266	X-RAY DIFFRACTION	96
2.082-2.1118	0.2301	175	0.1698	3270	X-RAY DIFFRACTION	97
2.1118-2.1433	0.2104	163	0.1709	3249	X-RAY DIFFRACTION	94
2.1433-2.1768	0.2197	173	0.1637	3314	X-RAY DIFFRACTION	97
2.1768-2.2124	0.2184	181	0.16	3348	X-RAY DIFFRACTION	98
2.2124-2.2506	0.1992	157	0.1647	3319	X-RAY DIFFRACTION	94
2.2506-2.2915	0.209	183	0.1617	3325	X-RAY DIFFRACTION	98
2.2915-2.3356	0.2022	200	0.1543	3317	X-RAY DIFFRACTION	97
2.3356-2.3832	0.206	162	0.1597	3296	X-RAY DIFFRACTION	96
2.3832-2.435	0.2067	166	0.1556	3408	X-RAY DIFFRACTION	99
2.435-2.4917	0.1973	176	0.1539	3335	X-RAY DIFFRACTION	96
2.4917-2.5539	0.2262	179	0.1582	3387	X-RAY DIFFRACTION	100
2.5539-2.623	0.2159	170	0.1612	3367	X-RAY DIFFRACTION	96
2.623-2.7001	0.202	160	0.16	3422	X-RAY DIFFRACTION	100
2.7001-2.7872	0.1872	189	0.1566	3347	X-RAY DIFFRACTION	97
2.7872-2.8868	0.2065	166	0.1543	3429	X-RAY DIFFRACTION	99
2.8868-3.0023	0.189	164	0.1593	3393	X-RAY DIFFRACTION	98
3.0023-3.1388	0.1974	195	0.1477	3339	X-RAY DIFFRACTION	97
3.1388-3.3041	0.164	163	0.1397	3421	X-RAY DIFFRACTION	98
3.3041-3.5109	0.1942	174	0.1388	3385	X-RAY DIFFRACTION	98
3.5109-3.7816	0.1608	184	0.142	3374	X-RAY DIFFRACTION	97
3.7816-4.1615	0.1839	175	0.1376	3369	X-RAY DIFFRACTION	96
4.1615-4.7621	0.1579	191	0.1399	3317	X-RAY DIFFRACTION	96
4.7621-5.9935	0.1715	176	0.1756	3373	X-RAY DIFFRACTION	95
5.9935-32.4792	0.2122	163	0.1881	3408	X-RAY DIFFRACTION	93

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	1.3596	0.0705	0.0443	0.8829	-0.138	1.7092	0.0466	-0.2056	0.1715	0.1025	0.0434	0.0917	-0.1754	-0.0075	-0.0869	0.1356	-0.0223	0.0315	0.1349	-0.0104	0.0967	18.8399	9.5734	35.9181
2	0.9847	0.2399	0.0057	0.6558	-0.096	0.7887	0.0119	-0.0858	-0.0715	0.038	-0.0336	-0.0232	0.0753	0.0022	0.0176	0.0818	-0.0052	0.0184	0.081	0.0288	0.0845	26.3769	-3.6797	16.5068
3	1.179	1.2918	0.3059	2.6256	-0.192	2.3037	-0.1341	0.2377	0.4104	-0.1015	0.0165	0.5299	-0.2509	-0.1426	0.0019	0.1282	-0.0156	0.0283	0.1105	0.0373	0.1729	7.4924	8.2654	25.4838
4	2.1857	1.0605	0.6865	0.7393	0.2788	1.2582	0.0988	-0.2021	-0.4372	0.1559	-0.0444	-0.0308	0.1602	0.0711	-0.0056	0.1667	-0.0331	0.0698	0.1487	0.0509	0.1537	12.0691	-6.7963	34.8097
5	1.4459	-0.1287	-0.0504	1.9207	-0.1349	3.2336	0.0335	-0.263	0.02	0.1709	-0.1501	0.3004	-0.0776	-0.3507	0.048	0.1035	-0.0153	0.0586	0.2241	0.0015	0.1734	-2.7243	-1.4921	29.2475
6	1.6718	0.1019	0.3412	1.5462	0.2733	0.847	0.0522	0.1137	-0.1077	-0.0879	0.0446	-0.119	0.0435	0.1588	-0.0276	0.0938	0.0054	0.0738	0.1134	0.0232	0.0865	35.9227	-3.9421	-16.813
7	0.6414	0.0375	0.0349	0.6699	-0.1294	0.8544	0.0026	-0.0013	0.0516	-0.0054	-0.0089	0.0302	-0.0646	-0.0059	0.0052	0.0665	-0.0056	0.0238	0.0639	0.0203	0.0795	23.0279	7.8485	0.4631
8	1.5574	-0.2374	0.163	2.6755	-0.6066	2.2496	0.0218	-0.1075	-0.3305	0.1551	0.0154	-0.0862	0.1853	0.0659	-0.0225	0.0961	-0.0097	0.0058	0.0952	0.031	0.1356	25.7143	-13.0217	-10.8299
9	2.2621	1.7019	0.1952	2.0322	-0.3106	1.1647	-0.0181	0.1612	0.3431	-0.1587	0.1059	0.474	-0.0968	-0.0945	-0.0973	0.096	0.0198	-0.0016	0.1053	0.0116	0.1262	18.4281	-0.1801	-21.5297
10	2.4235	0.2568	-0.1807	3.2403	-1.3336	3.3686	0.0215	0.2371	-0.2497	-0.2804	0.1052	0.0685	0.2464	-0.184	-0.1167	0.108	-0.0221	-0.0309	0.0932	-0.0105	0.1221	13.6495	-15.4787	-19.2714
11	1.7177	-0.6183	0.3716	1.7612	0.4261	0.9804	0.0596	0.2203	-0.0772	-0.1914	-0.039	0.0158	0.0457	0.1075	0.0041	0.1514	0.0077	0.0541	0.1595	0.0097	0.0871	11.1615	6.8926	63.9835
12	1.1352	-0.1347	0.0293	0.9223	-0.1318	0.9061	0.0011	0.0877	0.1127	-0.003	-0.0473	-0.0714	-0.1778	0.0958	0.0343	0.1481	-0.0261	0.0192	0.0982	0.0358	0.0991	9.2934	21.8088	82.9807
13	3.1489	0.6147	-0.271	3.8482	-0.4885	2.9519	-0.0087	-0.083	-0.2428	-0.2695	-0.1696	0.3549	-0.0252	-0.1505	0.1409	0.129	0.0469	-0.0041	0.1235	-0.0141	0.132	-2.813	10.2236	65.5609
14	2.6689	0.4931	0.1854	0.0958	0.0356	1.189	0.0951	0.0549	0.5769	-0.2928	-0.1768	-0.1564	-0.3356	0.0857	0.0247	0.2762	0.006	0.0444	0.1617	0.0727	0.1999	6.2082	25.1095	60
15	1.2706	0.3984	-0.3887	2.6403	-0.7348	2.7156	0.0906	0.4188	0.0437	-0.3908	-0.1436	0.4057	-0.0381	-0.2565	0.0625	0.2326	0.0599	-0.1115	0.2826	0.0009	0.2007	-10.5061	19.7789	58.1289
16	1.154	-0.4022	0.456	1.4509	0.0539	1.6568	-0.0875	0.0621	0.1261	0.1473	0.0785	-0.0942	-0.0431	0.1014	-0.0151	0.1446	-0.004	0.0123	0.1197	0.0228	0.086	1.0576	22.1909	116.3212
17	0.8867	0.0367	-0.0598	0.4797	0.0133	0.7828	-0.0431	-0.0657	-0.0612	-0.0216	0.0188	0.0274	0.0083	-0.0604	0.0242	0.1298	-0.0016	0.0179	0.0794	0.0208	0.0797	-1.7121	10.2715	95.1167
18	2.3188	0.0086	0.297	0.8367	0.146	1.2262	-0.1496	-0.0111	0.3838	-0.1339	-0.0206	-0.2355	-0.1514	0.1028	0.1105	0.1759	-0.019	0.008	0.1303	0.0613	0.1407	-5.1448	31.2629	106.4195
19	1.2241	-0.9785	0.1341	1.7031	-1.3385	1.6556	0.1937	-0.2049	-0.3783	-0.2211	0.0882	0.4601	0.3079	-0.3139	-0.2516	0.1356	-0.0272	-0.0123	0.1711	0.0642	0.1867	-16.9144	18.251	111.5848
20	2.6004	0.1658	0.3145	2.7593	-1.0187	3.753	-0.0419	-0.1398	0.2662	0.3026	0.0823	0.1993	-0.2411	-0.3803	-0.0275	0.158	0.033	0.0482	0.1488	0.0348	0.1815	-19.097	34.363	106.1833

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 31:142
2	X-RAY DIFFRACTION	2	CHAIN A AND RESID 143:316
3	X-RAY DIFFRACTION	3	CHAIN A AND RESID 317:337
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 338:367
5	X-RAY DIFFRACTION	5	CHAIN A AND RESID 368:399
6	X-RAY DIFFRACTION	6	CHAIN B AND RESID 36:142
7	X-RAY DIFFRACTION	7	CHAIN B AND RESID 143:316
8	X-RAY DIFFRACTION	8	CHAIN B AND RESID 317:337
9	X-RAY DIFFRACTION	9	CHAIN B AND RESID 338:367
10	X-RAY DIFFRACTION	10	CHAIN B AND RESID 368:400
11	X-RAY DIFFRACTION	11	CHAIN C AND RESID 41:142
12	X-RAY DIFFRACTION	12	CHAIN C AND RESID 143:316
13	X-RAY DIFFRACTION	13	CHAIN C AND RESID 317:337
14	X-RAY DIFFRACTION	14	CHAIN C AND RESID 338:367
15	X-RAY DIFFRACTION	15	CHAIN C AND RESID 368:396
16	X-RAY DIFFRACTION	16	CHAIN D AND RESID 38:142
17	X-RAY DIFFRACTION	17	CHAIN D AND RESID 143:316
18	X-RAY DIFFRACTION	18	CHAIN D AND RESID 317:337
19	X-RAY DIFFRACTION	19	CHAIN D AND RESID 338:367
20	X-RAY DIFFRACTION	20	CHAIN D AND RESID 368:397

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi