PDB-5ayv: Crystal structure of archaeal ketopantoate reductase complexed wi...

ID or keywords:

Entry

Database: PDB / ID: 5ayv

Title

Crystal structure of archaeal ketopantoate reductase complexed with coenzyme A and 2-oxopantoate

Components

2-dehydropantoate 2-reductase

Keywords

OXIDOREDUCTASE / ketopantoate reductase / coenzyme A / feedback inhibition

Function / homology

Function and homology information

2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / coenzyme A biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function

Biological species

Thermococcus kodakarensis KOD1 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.647 Å

Authors

Aikawa, Y. / Nishitani, Y. / Miki, K.

Citation

Journal: Proteins / Year: 2016
Title: Crystal structure of archaeal ketopantoate reductase complexed with coenzyme a and 2-oxopantoate provides structural insights into feedback regulation
Authors: Aikawa, Y. / Nishitani, Y. / Tomita, H. / Atomi, H. / Miki, K.

History

Deposition	Sep 8, 2015	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2016	Group: Database references
Revision 1.2	Feb 26, 2020	Group: Data collection / Database references / Derived calculations Category: citation / diffrn_source / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 8, 2023	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 1.4	Apr 3, 2024	Group: Derived calculations / Category: struct_conn / struct_conn_type Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ayv.cif.gz	261.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5ayv_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ayv_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5ayv_validation.xml.gz	29.7 KB	Display
Data in CIF	5ayv_validation.cif.gz	43.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayv ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayv	HTTPS FTP

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Related structure data

Related structure data	2ofpS S: Starting model for refinement
Similar structure data	5hws-1 3hwr-d 5hws-2 5x20-1 4yca-d 3eqr-1 3wfj-2 2boy-4 6do1-2 6dqe-2 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	#127 - Jul 2010 Crystallins similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#127 - Jul 2010
Crystallins
similarity (2)
#111 - Mar 2009
Hydrogenase
similarity (1)
#228 - Dec 2018
Directed Evolution of Enzymes
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#93 - Sep 2007
Citrate Synthase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#216 - Dec 2017
Biodegradable Plastic
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)

Deposited unit

A: 2-dehydropantoate 2-reductase

B: 2-dehydropantoate 2-reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.519, 70.822, 163.902
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	2-dehydropantoate 2-reductase Mass: 34088.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea) Strain: KOD1 / Gene: TK1968 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q5JGC2, 2-dehydropantoate 2-reductase

#1: Protein

2-dehydropantoate 2-reductase

Mass: 34088.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: TK1968 / Plasmid: pET21A / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q5JGC2, 2-dehydropantoate 2-reductase

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Non-polymers , 6 types, 485 molecules

#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#5: Chemical	ChemComp-KPL / KETOPANTOATE / 2-DEHYDROPANTOATE Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₀O₄
#6: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.3 Å³/Da / Density % sol: 46.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: acetate, MPD

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.647→50 Å / Num. obs: 73909 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 6 % / B_iso Wilson estimate: 24 Å² / Net I/σ(I): 20.2
Reflection shell	Resolution: 1.647→1.71 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OFP

2ofp

Resolution: 1.647→32.535 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1887	3649	4.94 %
R_work	0.1687	-	-
obs	0.1697	73795	96.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 28.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.647→32.535 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4683	0	142	475	5300

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4921
X-RAY DIFFRACTION	f_angle_d	0.904	6690
X-RAY DIFFRACTION	f_dihedral_angle_d	14.772	1772
X-RAY DIFFRACTION	f_chiral_restr	0.043	752
X-RAY DIFFRACTION	f_plane_restr	0.004	847

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 (%)
1.6474-1.6691	0.2632	124	0.253	2677	X-RAY DIFFRACTION	97
1.6691-1.692	0.2576	139	0.2417	2657	X-RAY DIFFRACTION	98
1.692-1.7161	0.2996	150	0.2385	2697	X-RAY DIFFRACTION	99
1.7161-1.7417	0.2597	158	0.2286	2700	X-RAY DIFFRACTION	98
1.7417-1.769	0.2535	125	0.2177	2674	X-RAY DIFFRACTION	98
1.769-1.798	0.2947	122	0.209	2723	X-RAY DIFFRACTION	98
1.798-1.829	0.2575	131	0.2062	2686	X-RAY DIFFRACTION	98
1.829-1.8622	0.2407	157	0.1995	2677	X-RAY DIFFRACTION	97
1.8622-1.898	0.2374	154	0.1956	2647	X-RAY DIFFRACTION	97
1.898-1.9368	0.1929	134	0.1959	2685	X-RAY DIFFRACTION	97
1.9368-1.9789	0.2252	133	0.1867	2667	X-RAY DIFFRACTION	96
1.9789-2.0249	0.2203	129	0.1898	2631	X-RAY DIFFRACTION	96
2.0249-2.0755	0.2219	123	0.185	2668	X-RAY DIFFRACTION	96
2.0755-2.1316	0.1872	128	0.1806	2652	X-RAY DIFFRACTION	95
2.1316-2.1943	0.1878	138	0.1754	2636	X-RAY DIFFRACTION	95
2.1943-2.2651	0.1945	142	0.1665	2615	X-RAY DIFFRACTION	94
2.2651-2.3461	0.2121	142	0.1741	2619	X-RAY DIFFRACTION	94
2.3461-2.44	0.1933	147	0.1675	2606	X-RAY DIFFRACTION	94
2.44-2.551	0.1984	139	0.1653	2635	X-RAY DIFFRACTION	94
2.551-2.6854	0.1853	149	0.1705	2639	X-RAY DIFFRACTION	96
2.6854-2.8536	0.1659	140	0.1682	2699	X-RAY DIFFRACTION	96
2.8536-3.0738	0.1966	134	0.1599	2763	X-RAY DIFFRACTION	98
3.0738-3.3828	0.1576	157	0.1598	2807	X-RAY DIFFRACTION	99
3.3828-3.8716	0.156	144	0.1406	2839	X-RAY DIFFRACTION	100
3.8716-4.8752	0.1626	142	0.1364	2889	X-RAY DIFFRACTION	100
4.8752-32.5411	0.188	168	0.182	2958	X-RAY DIFFRACTION	99

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	4.1709	1.0284	0.894	3.2524	0.6434	3.9502	-0.005	-0.3055	-0.0677	0.4004	-0.0769	0.2261	0.58	-0.1428	0.0772	0.3164	0.0251	0.0203	0.2007	-0.0189	0.1505	-13.9844	-13.1252	41.8647
2	8.1757	-2.8716	3.6213	4.0086	-1.0248	7.4055	-0.0947	-0.1011	0.4645	0.23	0.0411	-0.1092	-0.2274	0.1045	0.0548	0.1843	0.0102	0.0217	0.1611	0.0082	0.1566	-6.7538	-0.706	36.755
3	2.0837	0.4766	-0.7108	2.4862	-0.0596	2.7794	-0.0171	0.0809	-0.1017	0.0249	-0.0263	-0.0362	0.3227	0.2317	0.0437	0.1919	0.0515	-0.029	0.2069	-0.0177	0.1346	-7.2992	-8.8317	29.4625
4	5.2334	1.3321	-0.8218	1.7174	-1.4084	3.6671	-0.1814	-0.0358	-0.4264	0.1288	0.0715	-0.4149	0.9416	0.6409	0.1085	0.4237	0.2274	-0.0543	0.3663	-0.0549	0.2647	2.1559	-16.164	31.8411
5	6.342	-0.2377	2.9505	0.9531	-0.3049	2.5685	0.0843	-0.2275	-0.3094	-0.1387	0.0382	0.0069	0.1958	0.0949	-0.1476	0.2268	0.0266	0.0013	0.2227	0.0071	0.1778	-10.7412	-6.6579	15.1405
6	4.7756	1.1911	1.5251	2.6352	0.5873	2.2169	0.1832	0.3275	-0.8473	-0.0636	0.0732	-0.3007	0.4854	0.4655	-0.2251	0.3087	0.1216	-0.0137	0.253	-0.0237	0.275	-9.1508	-9.9405	8.3957
7	5.942	2.3217	1.7295	7.3152	1.3537	4.2699	0.1372	-0.5685	-0.4149	0.2952	-0.1655	0.3882	0.4525	-0.3998	0.0225	0.1946	0.0146	0.0036	0.2404	0.0729	0.2034	-21.7143	-7.5195	19.7372
8	7.639	7.4901	-4.4251	7.4594	-3.9599	7.9337	0.062	-0.3268	0.2607	0.1635	-0.1124	-0.0154	-0.3448	0.203	-0.0035	0.1812	0.0464	-0.0398	0.1948	-0.0069	0.2057	-7.0991	6.7805	12.6668
9	5.8092	0.4794	-3.5488	7.5905	-0.1268	8.5954	0.1503	-0.3106	0.1204	0.4535	-0.0196	0.4706	0.0112	-0.3196	-0.1678	0.2063	0.0138	-0.0382	0.1851	-0.012	0.1943	-22.4156	2.9145	13.3394
10	2.0424	-0.1993	-0.7366	3.2977	-0.0524	2.6714	-0.0933	0.1349	-0.2185	-0.0964	-0.0348	0.4008	0.2712	-0.3666	0.1178	0.1256	-0.0248	-0.0103	0.1495	-0.0368	0.207	-47.5646	4.5065	-18.8302
11	3.1501	-0.5878	1.8296	2.2555	-2.2861	4.6237	0.2018	0.3531	-0.2989	-0.366	-0.0912	-0.0042	0.5246	0.0988	-0.0823	0.1776	0.0354	0.015	0.1672	-0.0446	0.1571	-32.3572	2.3211	-24.2876
12	1.1222	-0.4006	0.6959	0.9036	-0.3896	2.7959	-0.0223	0.1425	0.0638	-0.0183	-0.0387	0.0446	-0.1447	0.049	0.0737	0.1103	-0.0094	-0.0046	0.0917	-0.015	0.1544	-34.2167	12.3593	-14.7525
13	3.6697	2.3439	-1.3678	3.1083	-1.2473	4.8589	0.211	-0.3879	0.1014	0.3819	-0.1621	-0.0884	-0.3707	0.3053	-0.0831	0.1663	0.0205	-0.047	0.0811	-0.0171	0.1835	-22.831	11.0453	2.6574
14	7.7478	-1.72	-2.1836	4.3491	1.1448	4.4835	0.215	0.3061	0.5315	0.0025	-0.0317	-0.2299	-0.4839	0.1392	-0.1868	0.1227	-0.0185	-0.0212	0.1183	-0.0002	0.1492	-25.6049	17.7909	-6.2146
15	5.8913	0.4176	-1.1591	4.7335	-1.1134	3.0576	0.1086	-0.0273	-0.4334	-0.0077	-0.0603	0.3636	0.2723	-0.0472	0.0072	0.1347	0.0011	-0.0466	0.1015	-0.001	0.1498	-34.0336	0.3288	-3.3063
16	9.5625	0.7118	-4.3305	7.1417	-1.0927	8.9906	-0.1211	0.2265	-0.5561	-0.2033	-0.0503	-0.9614	0.5988	0.6314	0.1532	0.1831	0.0664	0.0102	0.1937	-0.0178	0.2514	-13.9689	2.6591	-9.4909
17	6.482	4.7003	0.3837	9.6948	0.388	4.5745	0.064	0.0748	-0.4892	-0.0679	-0.0002	0.131	0.5789	-0.2376	-0.0593	0.2047	0.0258	-0.0452	0.1229	-0.0102	0.2043	-26.0404	-5.7558	-0.4169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 97 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 98 through 150 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 151 through 172 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 173 through 194 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 195 through 243 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 244 through 266 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 267 through 281 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 282 through 300 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 74 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 75 through 110 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 111 through 194 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 195 through 224 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 225 through 243 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 244 through 266 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 267 through 281 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 282 through 303 )

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