PDB-5t2u: short chain dehydrogenase/reductase family protein

ID or keywords:

Entry

Database: PDB / ID: 5t2u

Title

short chain dehydrogenase/reductase family protein

Components

Oxidoreductase, short chain dehydrogenase/reductase family protein

Keywords

OXIDOREDUCTASE / FabG / mycobacterium / fatty acids

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Mickael, B. / Van Wyk, N. / Baneres-Roquet, F. / Yann, G. / Laurent, K.

Citation

Journal: Biochem. J. / Year: 2017
Title: Binding of NADP(+) triggers an open-to-closed transition in a mycobacterial FabG beta-ketoacyl-ACP reductase.
Authors: Blaise, M. / Van Wyk, N. / Baneres-Roquet, F. / Guerardel, Y. / Kremer, L.

History

Deposition	Aug 24, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2017	Group: Database references
Revision 1.2	Jan 17, 2024	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t2u.cif.gz	371.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5t2u.ent.gz	304.6 KB	Display	PDB format
PDBx/mmJSON format	5t2u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5t2u_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5t2u_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5t2u_validation.xml.gz	41.4 KB	Display
Data in CIF	5t2u_validation.cif.gz	60.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t2/5t2u ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t2u	HTTPS FTP

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Related structure data

Related structure data	5t2vSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3enn-d 4fgs-d 5h5x-2 6ihi-d 6d9y-1 3gaf-1 3lyl-d 5vrn-8 3guy-1 1dfh-1 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	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Oxidoreductase, short chain dehydrogenase/reductase family protein

B: Oxidoreductase, short chain dehydrogenase/reductase family protein

C: Oxidoreductase, short chain dehydrogenase/reductase family protein

D: Oxidoreductase, short chain dehydrogenase/reductase family protein

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	65.010, 116.110, 132.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Oxidoreductase, short chain dehydrogenase/reductase family protein / Short-chain dehydrogenase/reductase SDR Mass: 25604.475 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6753, MSMEI_6571 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0R723
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.45 Å³/Da / Density % sol: 49.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Na citrate tribasic dehydrate, 20% peg3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.2→19.91 Å / Num. obs: 51201 / % possible obs: 98.7 % / Redundancy: 3.7 % / R_rim(I) all: 0.176 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.28 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5T2V

5t2v

Resolution: 2.2→19.91 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.82

	R_factor	Num. reflection	% reflection
R_free	0.2177	2000	3.91 %
R_work	0.163	-	-
obs	0.1651	51200	98.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→19.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6906	0	192	738	7836

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7226
X-RAY DIFFRACTION	f_angle_d	0.693	9884
X-RAY DIFFRACTION	f_dihedral_angle_d	13.467	2515
X-RAY DIFFRACTION	f_chiral_restr	0.061	1155
X-RAY DIFFRACTION	f_plane_restr	0.004	1295

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	Highest resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.2-2.2549		0.2778	143	0.2316	3507	99
2.2549-2.3158		0.2745	140	0.2194	3441	98
2.3158-2.3838		0.3064	138	0.2074	3414	98
2.3838-2.4606		0.2603	141	0.2009	3464	99
2.4606-2.5484		0.2485	142	0.1915	3495	100
2.5484-2.6502		0.2909	143	0.1937	3518	100
2.6502-2.7705		0.2639	142	0.1907	3498	99
2.7705-2.9162		0.253	142	0.1829	3491	99
2.9162-3.0983		0.2194	145	0.169	3548	100
3.0983-3.3365		0.2203	141	0.158	3499	99
3.3365-3.6703		0.1925	144	0.1455	3528	99
3.6703-4.1971		0.1688	144	0.132	3549	99
4.1971-5.2716		0.1579	145	0.1169	3555	98
	5.2716	0.181	150	0.1365	3693	98

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	6.486	2.7337	0.6226	5.3789	1.1496	3.2368	-0.1511	0.1645	0.363	-0.1502	-0.0356	0.3705	-0.3006	-0.2665	0.1673	0.1368	0.0501	0.0337	0.2171	-0.0872	0.2256	-27.907	29.317	-20.0651
2	1.6113	-1.101	0.1826	1.3794	0.7642	2.6383	-0.2483	-0.6658	0.2165	0.167	0.0578	0.1893	-0.1333	-0.4379	0.1606	0.1917	0.0271	0.035	0.3988	-0.1112	0.3202	-27.2983	25.1386	-9.8515
3	2.3151	0.6067	1.0932	1.165	0.8495	1.2327	0.0015	-0.2055	0.1001	0.0335	-0.0564	0.0638	-0.0186	-0.1641	0.0611	0.1379	-0.0009	0.0263	0.1652	-0.0369	0.151	-11.234	18.6638	-15.2525
4	1.7581	0.0723	-0.591	2.5092	-0.1802	2.216	-0.0044	-0.1484	0.3302	0.2671	0.0111	-0.0586	-0.2231	0.0679	0.0215	0.1639	0.0163	-0.0074	0.1756	-0.0409	0.1971	-12.2658	31.0651	-24.2213
5	3.3515	1.0526	1.2215	7.8749	0.3129	6.0634	0.0595	0.2036	0.2893	0.2505	0.0155	0.4964	0.0246	-0.6982	-0.0506	0.1491	0.0499	-0.0423	0.2637	0.0503	0.2842	-23.9732	32.5902	-46.1907
6	4.1934	-1.1985	-1.1272	1.2512	-0.5532	3.9687	0.1683	0.552	0.1073	-0.1655	-0.1102	0.1693	-0.2185	-0.1526	-0.0736	0.2655	0.0334	-0.081	0.204	0.0725	0.2995	-18.807	33.8759	-56.291
7	0.7978	-0.9421	-0.1672	4.3471	1.4368	1.2963	0.0193	0.155	0.0145	-0.0409	-0.043	0.1691	0.0261	-0.0304	0.025	0.138	-0.0072	-0.008	0.1696	0.0238	0.1481	-5.4064	24.685	-48.0751
8	3.3155	1.3087	0.3706	3.3034	-1.1388	2.1257	-0.016	0.3567	-0.328	-0.2614	0.0967	0.0997	0.4309	-0.0938	-0.1172	0.1633	0.0173	0.0086	0.1877	-0.0529	0.2056	-18.3571	15.2044	-43.3068
9	1.214	1.5826	0.163	5.1811	-0.3233	1.3221	0.0505	0.1135	0.3049	0.1071	-0.152	0.296	-0.0651	-0.1075	0.078	0.1447	0.0123	0.0266	0.1799	-0.0141	0.1213	-16.6287	25.0683	-35.8023
10	5.0242	4.9077	-0.9244	6.8664	0.0186	3.0037	-0.1809	-0.1625	-0.3304	-0.2432	0.0525	-0.3731	0.2744	0.2321	0.148	0.1861	0.0721	-0.0422	0.2066	0.0511	0.1608	19.228	2.8228	-16.6858
11	5.2128	-1.18	-1.3291	3.5844	-1.0773	4.0784	-0.167	-0.2801	-0.4273	0.1414	-0.0755	-0.0334	0.1955	0.1126	0.1949	0.1562	-0.0381	-0.0174	0.1983	-0.0074	0.1611	14.9041	3.0025	-6.3264
12	3.7669	1.01	0.1407	1.283	0.1375	0.6058	-0.0245	-0.1659	-0.0983	0.0415	0.0307	-0.0085	0.039	-0.0498	-0.0121	0.1469	-0.0108	0.0072	0.1235	-0.0261	0.1096	1.186	12.062	-14.3083
13	1.746	0.7326	0.406	3.6412	-0.1491	2.1634	0.0846	-0.1129	-0.1859	-0.0465	-0.0319	0.2191	0.253	-0.1913	-0.0334	0.1444	0.0007	0.0253	0.1541	-0.0166	0.1309	6.0544	3.6845	-26.2352
14	4.9873	1.5271	-0.3258	7.6786	-2.742	5.736	0.0227	-0.0289	-0.4957	-0.1028	-0.1889	-0.3614	0.4265	0.6274	0.1241	0.1838	0.0766	0.0568	0.32	-0.0329	0.1809	23.338	6.875	-43.8596
15	4.0573	0.1031	0.0239	2.0734	-0.919	3.7375	-0.0904	0.3943	-0.0399	-0.2039	-0.0999	-0.2022	0.2295	0.5101	0.1524	0.1919	0.0222	0.0212	0.2857	-0.0006	0.1922	23.6586	12.4289	-50.5163
16	0.6287	-0.1054	-0.0069	4.7084	-0.3955	0.6303	-0.015	0.1452	0.0415	-0.2003	-0.0087	-0.1814	0.033	0.0145	0.0236	0.1487	-0.0076	-0.0207	0.1818	0.0039	0.1391	7.1559	18.4338	-47.0725
17	2.6934	0.0327	0.0425	3.0147	1.0248	2.8787	-0.0118	0.1618	0.6321	-0.1439	0.0942	0.0757	-0.3254	0.3879	-0.0582	0.133	-0.0351	0.0273	0.2166	0.0404	0.1674	16.4856	21.7908	-39.689
18	4.2668	-0.3064	0.7365	6.7049	-0.5215	4.9434	-0.0106	0.2642	1.1057	-0.0355	0.1687	-0.0318	-1.1531	0.2236	-0.138	0.3168	-0.0534	0.035	0.1895	0.0378	0.3646	16.764	31.4746	-29.9813
19	1.623	1.1169	0.2695	4.7315	1.4327	2.3647	-0.0908	0.0671	-0.0454	-0.0255	0.1409	-0.1112	0.1424	0.2816	-0.0229	0.1252	0.0067	-0.0018	0.1492	0.0231	0.0882	13.548	13.1112	-32.7624

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 168 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 169 through 240 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 28 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 29 through 81 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 82 through 168 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 169 through 207 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 208 through 240 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 0 through 27 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 28 through 81 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 82 through 168 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 169 through 240 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 15 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 16 through 81 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 82 through 168 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 169 through 189 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 190 through 207 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 208 through 240 )

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