PDB-4aoy: Open CtIDH. The complex structures of Isocitrate dehydrogenase fr...

ID or keywords:

Entry

Database: PDB / ID: 4aoy

Title

Open CtIDH. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism

Components

ISOCITRATE DEHYDROGENASE [NADP]

Keywords

OXIDOREDUCTASE / TEMPERATURE ADAPTATION / THERMOPHILIC / PSYCHROPHILIC / NADP+ SELECTIVITY / DOMAIN MOVEMENTS

Function / homology

Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta / :

Function and homology information

Biological species

CLOSTRIDIUM THERMOCELLUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Leiros, H.-K.S. / Fedoy, A.-E. / Leiros, I. / Steen, I.H.

Citation

Journal: Febs Open Bio / Year: 2012
Title: The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism.
Authors: Leiros, H.K. / Fedoy, A.E. / Leiros, I. / Steen, I.H.

History

Deposition	Mar 30, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2013	Group: Database references
Revision 1.2	May 22, 2013	Group: Database references
Revision 1.3	May 15, 2019	Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4aoy.cif.gz	581.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4aoy.ent.gz	483.9 KB	Display	PDB format
PDBx/mmJSON format	4aoy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4aoy_validation.pdf.gz	464.1 KB	Display	wwPDB validaton report
Full document	4aoy_full_validation.pdf.gz	517.6 KB	Display
Data in XML	4aoy_validation.xml.gz	57 KB	Display
Data in CIF	4aoy_validation.cif.gz	77.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ao/4aoy ftp://data.pdbj.org/pub/pdb/validation_reports/ao/4aoy	HTTPS FTP

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Related structure data

Related structure data	4aouC 4aovC C: citing same article (ref.)
Similar structure data	6adi-d 6vg0-2 4hcx-d 6ajb-1 1zor-d 4jz6-1 6aja-1 5l57-1 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

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

B: ISOCITRATE DEHYDROGENASE [NADP]

D: ISOCITRATE DEHYDROGENASE [NADP]

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

2

A: ISOCITRATE DEHYDROGENASE [NADP]

C: ISOCITRATE DEHYDROGENASE [NADP]

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

Unit cell

Length a, b, c (Å)	56.130, 106.840, 154.500
Angle α, β, γ (deg.)	90.00, 93.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	C
2	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	2 - 401
2	1	1	4	B	2 - 401
1	1	2	4	C	2 - 401
2	1	2	4	D	2 - 401

NCS ensembles :

ID
1
2

#1: Protein	ISOCITRATE DEHYDROGENASE [NADP] Mass: 45842.199 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) CLOSTRIDIUM THERMOCELLUM (bacteria) References: UniProt: D1NLE9, isocitrate dehydrogenase (NADP+)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.52 Å³/Da / Density % sol: 51.22 % / Description: NONE
Crystal grow	Temperature: 310 K / Method: vapor diffusion, hanging drop Details: RESERVOIR SOLUTIONS OF 9-11% (W/V) POLYETHYLENE GLYCOL (PEG) PEG3350, AND 0.15 M AMMONIUM DIHYDROGEN CITRATE AT 37 DEG. C. PROTEIN AT 9.5 MG/ML

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0052
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0052 Å / Relative weight: 1
Reflection	Resolution: 2.35→20 Å / Num. obs: 75792 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / B_iso Wilson estimate: 46.42 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.35→2.48 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software

Name: REFMAC / Version: 5.5.0102 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25844	2010	2.7 %	RANDOM
R_work	0.20962	-	-	-
obs	0.21093	73524	99.74 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 49.016 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.31 Å²	0 Å²	-0.06 Å²
2-	-	0.25 Å²	0 Å²
3-	-	-	-0.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11590	0	0	88	11678

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	11806
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.67	1.949	15942
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.795	5	1478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.625	24.608	523
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.999	15	2046
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.393	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	1771
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	8843
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.746	1.5	7383
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.393	2	11861
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.272	3	4423
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.72	4.5	4081
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2816	medium positional	0.31	0.5
1	2	B	2816	medium positional	0.31	0.5
2	1	C	2851	medium positional	0.35	0.5
2	2	D	2851	medium positional	0.35	0.5
1	1	A	2816	medium thermal	0.81	2
1	2	B	2816	medium thermal	0.81	2
2	1	C	2851	medium thermal	0.93	2
2	2	D	2851	medium thermal	0.93	2

LS refinement shell

Resolution: 2.35→2.41 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	147	-
R_work	0.292	5309	-
obs	-	-	99.2 %

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	2.7151	-0.706	0.0496	2.7987	0.2424	1.4764	-0.0098	-0.0541	-0.2653	-0.1086	0.0416	0.217	0.197	-0.128	-0.0318	0.2158	0.015	0.0128	0.137	0.0191	0.134	24.451	-8.355	41.941
2	0.8419	-0.8911	0.959	1.0458	-0.9739	1.4182	-0.0306	-0.0385	0.0339	0.0086	0.0705	-0.0075	-0.2829	-0.0688	-0.0399	0.1946	0.0052	0.012	0.2008	0.0057	0.2045	33.91	0.267	67.202
3	2.1363	0.2272	0.7656	1.518	0.9757	2.5448	0.0959	-0.3932	0.0158	0.1064	-0.1362	0.0571	-0.0962	-0.2697	0.0403	0.3102	0.0283	0.0199	0.204	0.0561	0.2164	22.948	8.102	52.749
4	10.2549	-2.7142	-1.6772	6.496	0.5875	6.4183	0.1224	0.2362	-0.5908	0.0434	-0.3602	0.5222	-0.5046	-1.2613	0.2378	0.3751	0.0822	-0.1302	0.7171	0.0174	0.4625	1.372	1.406	39.75
5	2.5156	0.725	-0.3336	2.6809	0.2213	2.3984	0.0093	0.041	0.2552	-0.0046	-0.0364	0.0419	-0.1326	0.0407	0.027	0.2314	-0.0063	-0.02	0.1266	0.055	0.1257	29.029	50.466	34.819
6	0.6866	0.9763	-0.6997	1.6376	-0.8788	1.6591	0.0135	-0.0056	-0.0502	0.075	0.1027	0.1083	0.1836	-0.0377	-0.1162	0.1235	0.0324	0.0069	0.2617	-0.0046	0.2709	39.849	45.894	6.583
7	4.6769	0.4051	-0.9263	1.3242	1.5347	2.6688	0.2192	0.7101	-0.1226	-0.1087	-0.1288	-0.0056	0.1148	-0.134	-0.0904	0.4641	0.0752	-0.0437	0.3733	0.0269	0.3032	31.847	32.58	19.048
8	6.5585	0.1227	1.1141	3.2704	-0.0313	4.1069	0.0549	-0.3787	-0.103	-0.0172	-0.0588	0.6898	0.3359	-0.8418	0.0039	0.4041	-0.1041	0.0359	0.2814	0.0118	0.206	14.218	37.499	36.646
9	1.8686	-0.5355	1.5662	1.7191	0.0816	3.4098	-0.1158	0.102	0.2662	0.1159	0.1101	-0.2146	-0.2238	0.3213	0.0058	0.1543	-0.0004	0.0207	0.0871	-0.0065	0.1624	18.454	12.505	95.815
10	4.1491	1.4644	-1.2703	6.182	-4.3364	8.1689	0.0107	-0.0256	0.2774	-0.0426	-0.1271	0.0263	-0.1038	0.0998	0.1164	0.017	0.0003	-0.0433	0.1042	-0.0298	0.1583	44.902	-8.946	73.056
11	4.6274	-0.7555	2.1182	2.6566	-0.935	3.9672	0.1219	0.1871	-0.2057	-0.2466	-0.0405	0.1135	0.2001	-0.2002	-0.0815	0.0479	-0.0065	-0.0068	0.0379	-0.0226	0.1275	14.652	-9.586	79.603
12	1.4284	-1.7496	1.2858	5.8141	-1.5325	1.2689	-0.0393	0.1022	0.074	-0.0209	0.0782	0.1211	-0.0265	0.0297	-0.0389	0.1039	-0.0122	-0.0005	0.1341	0.0089	0.1696	6.389	14.105	88.756
13	1.6509	0.367	-1.3781	2.3641	0.1971	3.15	-0.1019	-0.1615	-0.2841	-0.1474	0.1312	-0.2831	0.1978	0.3839	-0.0293	0.135	-0.0123	0.0157	0.0967	0.0016	0.1583	23.688	29.291	-20.244
14	5.5242	1.1428	1.5545	0.4111	0.3104	1	0.0767	-0.3661	-0.056	0.0885	0.0216	-0.0629	0.1235	-0.134	-0.0982	0.1399	0.0136	0.0361	0.1531	-0.0334	0.1412	30.449	51.827	-1.984
15	0.6884	0.8705	-0.6974	3.4741	2.0027	5.5667	0.0232	-0.2877	-0.2387	0.4828	-0.0381	-0.3975	0.4768	0.3287	0.015	0.1296	0.0332	0.0288	0.2942	0.0545	0.2116	17.886	40.716	-2.842
16	1.7029	1.1725	-1.1573	7.438	-3.9773	3.7509	-0.0686	-0.0675	-0.0932	-0.0446	0.2747	0.4639	0.0576	-0.2948	-0.2062	0.0674	-0.0253	-0.0027	0.1106	-0.0053	0.1521	6.965	24.276	-13.81

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 117
2	X-RAY DIFFRACTION	2	A	118 - 212
3	X-RAY DIFFRACTION	3	A	213 - 375
4	X-RAY DIFFRACTION	4	A	376 - 401
5	X-RAY DIFFRACTION	5	B	3 - 117
6	X-RAY DIFFRACTION	6	B	118 - 191
7	X-RAY DIFFRACTION	7	B	192 - 326
8	X-RAY DIFFRACTION	8	B	327 - 399
9	X-RAY DIFFRACTION	9	C	3 - 132
10	X-RAY DIFFRACTION	10	C	141 - 180
11	X-RAY DIFFRACTION	11	C	181 - 264
12	X-RAY DIFFRACTION	12	C	265 - 402
13	X-RAY DIFFRACTION	13	D	2 - 124
14	X-RAY DIFFRACTION	14	D	125 - 241
15	X-RAY DIFFRACTION	15	D	242 - 326
16	X-RAY DIFFRACTION	16	D	327 - 402

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