PDB-8iwq: Pseudomoans Aerugiona Native Ketopantoate Reductase with glycerol

ID or keywords:

Entry

Database: PDB / ID: 8iwq

Title

Pseudomoans Aerugiona Native Ketopantoate Reductase with glycerol

Components

2-dehydropantoate 2-reductase

Keywords

OXIDOREDUCTASE / Ketopantoate Reductase / PanE / wildtype / pantothenate pathway protein.

Function / homology

:

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.191 Å

Authors

Choudhury, G.B. / Datta, S.

Funding support

India, 1items

Citation

Journal: Biochemistry / Year: 2024
Title: Implication of Molecular Constraints Facilitating the Functional Evolution of Pseudomonas aeruginosa KPR2 into a Versatile alpha-Keto-Acid Reductase.
Authors: Basu Choudhury, G. / Datta, S.

History

Deposition	Mar 30, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2024	Group: Database references / Category: citation / citation_author 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 / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8iwq.cif.gz	248.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8iwq.ent.gz	200.9 KB	Display	PDB format
PDBx/mmJSON format	8iwq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8iwq_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8iwq_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8iwq_validation.xml.gz	25 KB	Display
Data in CIF	8iwq_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iw/8iwq ftp://data.pdbj.org/pub/pdb/validation_reports/iw/8iwq	HTTPS FTP

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Related structure data

Related structure data	8iwgC 8ix9C 8ixhC 8ixmC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: 2-dehydropantoate 2-reductase

A: 2-dehydropantoate 2-reductase

hetero molecules

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

1

A: 2-dehydropantoate 2-reductase

hetero molecules

B: 2-dehydropantoate 2-reductase

hetero molecules

defined by author&software
Evidence: gel filtration
68.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.849, 47.497, 96.265
Angle α, β, γ (deg.)	90.00, 99.46, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	2-dehydropantoate 2-reductase Mass: 34205.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: K3T18_18035 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A8G2Q7Q1
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / Details: l

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
Detector	Type: Bruker PHOTON III / Detector: PIXEL / Date: Feb 6, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.19→27.09 Å / Num. obs: 30908 / % possible obs: 99.6 % / Redundancy: 5.2 % / CC_1/2: 0.995 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.19→2.27 Å / Num. unique obs: 2947 / CC_1/2: 0.703

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Processing

Software

Name	Version	Classification
PHENIX	1.14	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.191→26.864 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2422	3832	6.47 %
R_work	0.1951	-	-
obs	0.1981	28750	98.67 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.191→26.864 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4724	0	18	196	4938

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4848
X-RAY DIFFRACTION	f_angle_d	0.553	6575
X-RAY DIFFRACTION	f_dihedral_angle_d	9.27	2890
X-RAY DIFFRACTION	f_chiral_restr	0.038	711
X-RAY DIFFRACTION	f_plane_restr	0.004	872

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 (%)
2.191-2.2186	0.3315	125	0.3037	1774	X-RAY DIFFRACTION	85
2.2186-2.2478	0.3204	145	0.2791	2042	X-RAY DIFFRACTION	99
2.2478-2.2785	0.3539	140	0.2752	2099	X-RAY DIFFRACTION	99
2.2785-2.3111	0.2811	142	0.262	1996	X-RAY DIFFRACTION	99
2.3111-2.3455	0.3151	145	0.2568	2079	X-RAY DIFFRACTION	99
2.3455-2.3822	0.2762	148	0.2584	2071	X-RAY DIFFRACTION	99
2.3822-2.4212	0.3517	142	0.2637	2075	X-RAY DIFFRACTION	99
2.4212-2.4629	0.2684	138	0.2458	2039	X-RAY DIFFRACTION	99
2.4629-2.5077	0.2959	144	0.2409	2099	X-RAY DIFFRACTION	99
2.5077-2.5559	0.2665	143	0.2312	2031	X-RAY DIFFRACTION	99
2.5559-2.608	0.3087	139	0.2321	2026	X-RAY DIFFRACTION	99
2.608-2.6647	0.3106	143	0.2166	2070	X-RAY DIFFRACTION	99
2.6647-2.7266	0.2783	147	0.2213	2054	X-RAY DIFFRACTION	99
2.7266-2.7947	0.2753	141	0.2225	2095	X-RAY DIFFRACTION	99
2.7947-2.8702	0.2202	139	0.218	2026	X-RAY DIFFRACTION	99
2.8702-2.9545	0.2696	145	0.2128	2071	X-RAY DIFFRACTION	99
2.9545-3.0498	0.3073	142	0.2224	2070	X-RAY DIFFRACTION	99
3.0498-3.1586	0.2375	150	0.2077	2097	X-RAY DIFFRACTION	99
3.1586-3.2849	0.2728	141	0.2044	2017	X-RAY DIFFRACTION	99
3.2849-3.4341	0.2634	141	0.1874	2090	X-RAY DIFFRACTION	100
3.4341-3.6147	0.2187	147	0.1776	2042	X-RAY DIFFRACTION	99
3.6147-3.8406	0.2149	138	0.1656	2082	X-RAY DIFFRACTION	100
3.8406-4.1362	0.2174	144	0.1491	2067	X-RAY DIFFRACTION	99
4.1362-4.5506	0.1739	137	0.1369	2059	X-RAY DIFFRACTION	99
4.5506-5.2049	0.1829	143	0.1447	2090	X-RAY DIFFRACTION	100
5.2049-6.542	0.1996	140	0.1719	2066	X-RAY DIFFRACTION	100
6.542-26.864	0.1421	143	0.1397	2051	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	1.9199	-0.8412	1.1622	0.7191	-0.1716	1.4174	-0.1016	0.0174	0.492	0.0121	-0.2	-0.097	-0.5121	-0.1241	0.0709	0.2548	0.0992	-0.0302	0.1714	-0.042	0.2481	-5.8605	19.6932	-11.801
2	0.2011	-0.0047	0.1541	0.2234	0.0879	2.6511	0.0076	-0.0014	0.027	-0.0511	0.0129	-0.0081	0.001	-0.3115	-0.0239	0.128	0.0455	0.0097	0.1309	0.0119	0.1618	-6.2073	5.4573	-27.176
3	2.8302	-0.5458	0.8815	1.4668	0.3829	1.2353	-0.2667	-0.2843	0.0886	0.2858	0.1765	-0.2288	-0.176	-0.1401	0.026	0.2757	0.159	-0.0375	0.3482	-0.0752	0.2434	26.0929	-7.7964	-11.3328
4	0.9923	-0.8464	0.362	2.1855	0.6062	1.266	-0.1446	-0.0233	1.0885	-0.0701	-0.0192	-0.3596	-0.4546	0.0967	-0.0468	0.4088	0.1659	-0.1186	0.4843	-0.0789	0.6327	32.8534	-0.7494	-11.8037
5	0.9436	-0.5953	0.6785	0.5105	-0.269	0.662	-0.1832	-0.3794	0.6357	0.3007	0.1095	-0.507	-0.0747	0.0873	-0.0119	0.2855	0.1192	-0.0806	0.3679	-0.128	0.4819	28.2998	-2.2174	-10.3007
6	1.7318	0.0019	0.3424	0.4029	-0.2127	0.2277	-0.0329	0.083	0.1295	-0.0551	0.02	-0.3771	0.0219	0.1042	0.0148	0.1477	0.3048	-0.0305	0.3168	-0.0907	0.3097	37.1532	-14.1521	-17.6
7	1.4603	-0.3682	0.2501	0.3815	0.0549	0.8969	0.0438	-0.1134	-0.0238	0.07	-0.0056	-0.0621	0.2435	0.0571	0.1477	0.2649	0.2068	-0.0194	0.2645	-0.0164	0.1895	31.4675	-19.1272	-17.885
8	1.7801	-1.1804	0.5174	1.4332	-0.1585	1.2734	-0.0897	-0.2129	0.1329	-0.1241	0.0442	-0.1433	0.2062	0.1286	0.0506	0.1708	0.0846	0.0383	0.2388	0.0188	0.2252	23.6105	-13.2442	-17.6555
9	0.9833	-0.1318	0.1057	0.4334	0.1532	1.9042	-0.0322	-0.2878	-0.2342	0.1566	0.1625	0.1851	0.2572	-0.246	-0.0878	0.2581	0.0817	0.0414	0.2682	0.0643	0.2194	21.1293	-21.3499	-19.4389
10	1.0678	-0.6861	0.2565	1.803	-0.4961	1.4101	-0.1043	-0.1007	-0.2289	0.1697	0.2935	0.2997	0.1871	-0.3457	-0.1199	0.2098	-0.0048	0.003	0.2046	0.0419	0.1783	13.9893	-19.649	-35.7855
11	1.6949	-0.7557	-0.6315	0.7505	0.4903	0.4632	-0.3968	-0.2406	0.4241	0.1104	0.3954	-0.1859	-0.3892	-0.1026	-0.007	0.3938	0.0306	-0.1015	0.2426	-0.0065	0.2525	26.4763	-8.5582	-33.5429
12	1.6181	-0.4319	0.3525	1.285	-0.1488	2.1457	-0.1151	0.1751	-0.1311	0.2133	0.2523	-0.1879	0.2011	0.4023	-0.0497	0.1835	0.0533	-0.0251	0.25	-0.0223	0.1401	29.5174	-22.1648	-41.1552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 4 through 82 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 83 through 314 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 6 through 27 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 28 through 45 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 46 through 75 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 76 through 96 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 97 through 137 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 138 through 161 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 162 through 209 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 210 through 259 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 260 through 283 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 284 through 314 )

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