PDB-8ixm: Pseudomoans Aerugiona Wildtype Ketopantoate Reductase ternary com...

ID or keywords:

Entry

Database: PDB / ID: 8ixm

Title

Pseudomoans Aerugiona Wildtype Ketopantoate Reductase ternary complex with NADP+ and alpha-Ketoisocaproic acid

Components

2-dehydropantoate 2-reductase

Keywords

OXIDOREDUCTASE / PanE2 / ternary complex / Ketopantoate Reductase / alpha-Ketoisocaproic acid

Function / homology

2-OXO-4-METHYLPENTANOIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.96 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	Apr 1, 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	8ixm.cif.gz	262.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ixm.ent.gz	210.9 KB	Display	PDB format
PDBx/mmJSON format	8ixm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ixm_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8ixm_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8ixm_validation.xml.gz	29.6 KB	Display
Data in CIF	8ixm_validation.cif.gz	42 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ix/8ixm ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ixm	HTTPS FTP

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Related structure data

Related structure data	8iwgC 8iwqC 8ix9C 8ixhC 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

A: 2-dehydropantoate 2-reductase

B: 2-dehydropantoate 2-reductase

hetero molecules

70.5 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
70.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.587, 46.769, 95.775
Angle α, β, γ (deg.)	90.00, 98.11, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 424 molecules

#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₇NO₃S / Comment: pH buffer*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid Mass: 130.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.16 Å³/Da / Density % sol: 43.01 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 8000, 100mM CHES 9.5

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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: Mar 5, 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: 1.96→23.42 Å / Num. obs: 42331 / % possible obs: 99.7 % / Redundancy: 9.1 % / CC_1/2: 0.998 / Net I/σ(I): 12
Reflection shell	Resolution: 1.96→2.03 Å / Num. unique obs: 4206 / CC_1/2: 0.547

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→23.416 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2375	3516	4.28 %
R_work	0.192	-	-
obs	0.194	42230	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.96→23.416 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4715	0	133	418	5266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4980
X-RAY DIFFRACTION	f_angle_d	0.616	6773
X-RAY DIFFRACTION	f_dihedral_angle_d	6.572	3453
X-RAY DIFFRACTION	f_chiral_restr	0.038	727
X-RAY DIFFRACTION	f_plane_restr	0.004	885

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 (%)
1.96-1.9868	0.3683	144	0.3344	3146	X-RAY DIFFRACTION	100
1.9868-2.0152	0.384	139	0.3318	3178	X-RAY DIFFRACTION	100
2.0152-2.0453	0.3657	140	0.3128	3157	X-RAY DIFFRACTION	100
2.0453-2.0772	0.3077	135	0.2898	3129	X-RAY DIFFRACTION	100
2.0772-2.1113	0.3194	139	0.2691	3083	X-RAY DIFFRACTION	100
2.1113-2.1476	0.2512	143	0.2457	3190	X-RAY DIFFRACTION	100
2.1476-2.1867	0.2828	139	0.2357	3126	X-RAY DIFFRACTION	100
2.1867-2.2287	0.2469	144	0.2291	3192	X-RAY DIFFRACTION	100
2.2287-2.2741	0.3164	137	0.2324	3112	X-RAY DIFFRACTION	100
2.2741-2.3235	0.2887	140	0.2224	3159	X-RAY DIFFRACTION	100
2.3235-2.3775	0.2781	140	0.2123	3093	X-RAY DIFFRACTION	100
2.3775-2.4369	0.2549	142	0.2122	3155	X-RAY DIFFRACTION	100
2.4369-2.5028	0.2234	142	0.1946	3126	X-RAY DIFFRACTION	100
2.5028-2.5763	0.232	143	0.1977	3169	X-RAY DIFFRACTION	100
2.5763-2.6594	0.3072	139	0.203	3149	X-RAY DIFFRACTION	100
2.6594-2.7543	0.2548	144	0.1947	3155	X-RAY DIFFRACTION	100
2.7543-2.8644	0.2657	136	0.1958	3119	X-RAY DIFFRACTION	100
2.8644-2.9945	0.2329	140	0.1936	3134	X-RAY DIFFRACTION	100
2.9945-3.152	0.2096	146	0.1908	3165	X-RAY DIFFRACTION	100
3.152-3.3489	0.2416	145	0.1824	3141	X-RAY DIFFRACTION	100
3.3489-3.6067	0.2265	142	0.1659	3165	X-RAY DIFFRACTION	100
3.6067-3.968	0.1866	140	0.1471	3113	X-RAY DIFFRACTION	100
3.968-4.5386	0.2032	142	0.135	3136	X-RAY DIFFRACTION	100
4.5386-5.7045	0.1943	139	0.1425	3154	X-RAY DIFFRACTION	100
5.7045-23.416	0.1369	136	0.14	3127	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	1.605	-1.6977	-0.2937	1.9287	-0.4188	4.6057	-0.1854	-0.4476	0.708	0.3968	-0.0132	-0.4291	-0.5665	0.2343	-0.536	0.3784	0.15	-0.1648	0.2694	-0.2389	0.3775	22.3052	4.2496	34.458
2	1.2197	-0.3396	0.4325	0.6435	-0.088	0.4545	-0.1988	-0.311	0.6002	0.4586	0.1608	-0.3019	0.0853	0.3069	-0.084	0.2945	0.2	-0.0886	0.3162	-0.2074	0.364	24.763	-1.1417	32.7182
3	2.2246	-1.0736	0.1429	0.9432	0.3295	0.5629	0.0309	0.0463	-0.0679	0.1503	0.0389	-0.0255	0.2689	0.208	-0.0756	0.2772	0.2355	-0.0664	0.3067	-0.0514	0.1922	20.5358	-8.4809	28.8219
4	0.5887	-0.0535	0.0796	0.7371	0.6512	2.4894	-0.1109	-0.299	-0.1748	0.4645	0.1914	0.2025	0.2847	-0.4401	-0.0432	0.261	0.0883	0.046	0.284	0.0506	0.1876	10.5413	-12.9797	20.5607
5	8.7835	-2.485	-1.8571	0.7949	0.8817	1.7947	-0.0588	-0.035	0.8642	-0.022	0.109	-0.0439	-0.4146	0.0015	-0.1648	0.2936	0.119	-0.0539	0.1959	-0.0262	0.2505	14.1894	1.3703	14.3102
6	2.568	1.1822	0.2127	4.8137	0.7268	2.7975	-0.0344	-0.1329	-0.1662	0.3367	0.3228	-0.3041	0.3594	0.2679	-0.193	0.1749	0.1052	-0.0081	0.2185	-0.0609	0.11	22.0944	-15.7994	12.0493
7	1.482	1.368	1.0951	1.461	1.1327	1.9506	-0.2115	0.437	-0.0111	-0.1556	0.3016	-0.1583	0.0296	0.4967	-0.2269	0.0517	0.0778	0.0008	0.2963	0.0033	0.0959	22.949	-9.366	3.437
8	1.8381	-0.8976	0.5798	1.4346	0.8627	2.1036	-0.367	-0.461	1.0207	-0.2215	0.1143	-0.4578	-0.8984	-0.096	-0.3663	0.3682	0.1535	-0.02	0.1952	-0.1791	0.3599	-11.0932	26.2767	34.198
9	1.6421	0.0068	0.0767	0.4707	0.5742	2.5982	-0.0428	-0.2323	0.0418	0.0758	0.0774	0.0066	0.0118	-0.4782	-0.0178	0.1405	0.0652	0.0219	0.1393	0.0099	0.1537	-14.8755	11.4898	24.4226
10	2.1943	-0.1473	0.2682	1.6438	0.6957	2.5067	-0.2251	-0.088	-0.0169	0.3563	0.3182	0.3896	-0.1383	-0.4176	-0.0312	0.185	0.0807	0.0465	0.1818	0.0575	0.1473	-14.7945	12.3393	11.3112

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 111 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 112 through 161 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 162 through 258 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 259 through 273 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 274 through 297 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 298 through 314 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 96 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 97 through 240 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 241 through 314 )

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