PDB-8cxa: Crystal Structure of 3-oxoacyl-[acyl-carrier-protein] reductase f...

ID or keywords:

Entry

Database: PDB / ID: 8cxa

Title

Crystal Structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium smegmatis with bound NAD

Components

3-oxoacyl-[acyl-carrier-protein] reductase

Keywords

OXIDOREDUCTASE / SSGCID /

reductase /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Function and homology information

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of 3-oxoacyl-[acyl-carrier-protein] reductase with bound NAD
Authors: Bolejack, M.J. / deBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	May 20, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8cxa.cif.gz	399.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8cxa.ent.gz	325.9 KB	Display	PDB format
PDBx/mmJSON format	8cxa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cx/8cxa ftp://data.pdbj.org/pub/pdb/validation_reports/cx/8cxa	HTTPS FTP

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Related structure data

Related structure data	2ew8S S: Starting model for refinement
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: 3-oxoacyl-[acyl-carrier-protein] reductase

B: 3-oxoacyl-[acyl-carrier-protein] reductase

C: 3-oxoacyl-[acyl-carrier-protein] reductase

D: 3-oxoacyl-[acyl-carrier-protein] reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.860, 128.780, 60.900
Angle α, β, γ (deg.)	90.000, 96.030, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3-oxoacyl-[acyl-carrier-protein] reductase Mass: 29268.143 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: HS11286 / Gene: KPHS_35560 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.03 Å³/Da / Density % sol: 39.33 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein at 28.58 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03M magnesium chloride, 0.03M calcium chloride, and ...Details: Protein at 28.58 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03M magnesium chloride, 0.03M calcium chloride, and 0.1M MOPS/HEPES-Na pH 7.5 (Morpheus A8). Tray: 320494. Cryo: Direct. Puck: ndu6-9

Crystal

Density Matthews: 2.03 Å³/Da / Density % sol: 39.33 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein at 28.58 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03M magnesium chloride, 0.03M calcium chloride, and ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 8, 2022 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.65→45.25 Å / Num. obs: 110664 / % possible obs: 99.1 % / Redundancy: 3.11 % / B_iso Wilson estimate: 21.6 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.04 / R_rim(I) all: 0.047 / Χ²: 0.956 / Net I/σ(I): 15.41 / Num. measured all: 344196 / Scaling rejects: 5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.65-1.69	2.693	0.413	2.18	21635	8308	8034	0.858	0.515	96.7
1.69-1.74	3.084	0.345	2.92	24725	8050	8017	0.903	0.419	99.6
1.74-1.79	3.145	0.269	3.78	24410	7769	7761	0.933	0.325	99.9
1.79-1.84	3.146	0.211	4.79	23918	7606	7602	0.959	0.255	99.9
1.84-1.91	3.158	0.164	6.27	23138	7339	7326	0.973	0.197	99.8
1.91-1.97	3.155	0.124	8.06	22472	7127	7123	0.984	0.149	99.9
1.97-2.05	3.155	0.095	10.45	21421	6804	6790	0.99	0.114	99.8
2.05-2.13	3.16	0.075	12.75	20905	6634	6615	0.994	0.09	99.7
2.13-2.22	3.162	0.063	15.58	19910	6318	6296	0.995	0.076	99.7
2.22-2.33	3.139	0.055	17.92	19184	6138	6111	0.996	0.067	99.6
2.33-2.46	3.153	0.05	19.8	17990	5751	5706	0.997	0.06	99.2
2.46-2.61	3.15	0.042	23	16949	5419	5380	0.997	0.05	99.3
2.61-2.79	3.129	0.039	25.38	15929	5145	5091	0.997	0.046	99
2.79-3.01	3.137	0.034	28.55	14874	4796	4741	0.998	0.041	98.9
3.01-3.3	3.12	0.031	31.14	13493	4387	4324	0.998	0.037	98.6
3.3-3.69	3.095	0.028	33.79	12134	3989	3920	0.998	0.034	98.3
3.69-4.26	3.134	0.025	36.15	10861	3536	3466	0.999	0.03	98
4.26-5.22	3.171	0.023	37.49	9243	2985	2915	0.999	0.027	97.7
5.22-7.38	3.207	0.022	36.83	7226	2322	2253	0.999	0.026	97
7.38-45.25	3.168	0.022	38.92	3779	1286	1193	0.998	0.027	92.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	4487	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ew8

2ew8

Resolution: 1.65→45.25 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1822	2073	1.87 %
R_work	0.1574	108547	-
obs	0.1578	110620	99.04 %

Solvent computation

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

Displacement parameters

B_iso max: 84.3 Å² / B_iso mean: 29.3377 Å² / B_iso min: 11.67 Å²

Refinement step

Cycle: final / Resolution: 1.65→45.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7404	0	88	778	8270
B_iso mean	-	-	32.93	34.89	-
Num. residues	-	-	-	-	997

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.65-1.69	0.323	156	0.2745	7022	7178	96
1.69-1.73	0.2477	140	0.2344	7218	7358	99
1.73-1.78	0.252	160	0.2016	7248	7408	100
1.78-1.83	0.1966	115	0.1841	7272	7387	100
1.83-1.89	0.2216	121	0.1806	7342	7463	100
1.89-1.96	0.2002	148	0.1791	7225	7373	100
1.96-2.03	0.1898	136	0.1804	7371	7507	100
2.03-2.13	0.1858	119	0.1602	7239	7358	100
2.13-2.24	0.1963	136	0.1532	7265	7401	100
2.24-2.38	0.1613	150	0.1597	7255	7405	99
2.38-2.56	0.1881	135	0.1581	7225	7360	99
2.56-2.82	0.1904	146	0.1618	7271	7417	99
2.82-3.23	0.1845	128	0.1548	7250	7378	99
3.23-4.07	0.1455	142	0.1402	7224	7366	98
4.07-45.25	0.1703	141	0.1334	7120	7261	97

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	2.0654	-0.1573	0.8001	2.1927	0.3006	2.5525	-0.1851	0.248	0.3307	-0.484	-0.089	0.3535	-0.4603	-0.0229	0.2239	0.2674	0.0272	-0.0959	0.1873	0.0258	0.2527	20.087	5.0184	9.7664
2	2.828	0.3726	0.3732	1.5833	0.2377	0.9679	-0.0835	0.0683	0.2328	-0.0078	-0.019	0.0431	-0.1512	-0.0085	0.0943	0.1269	0.0095	0.0009	0.1077	0.0029	0.1315	31.9552	1.8273	22.9693
3	1.4283	-0.6293	-0.0021	2.1434	0.3666	1.9858	0.0633	0.2699	0.3751	-0.3241	-0.0465	-0.2656	-0.2456	0.2036	0.0053	0.1731	-0.0165	0.0326	0.168	0.0452	0.1708	37.1979	-7.9774	12.2523
4	2.559	-0.4418	0.5531	0.9037	0.6878	1.6096	0.287	-0.0719	-0.6129	-0.3983	-0.0371	0.7537	0.5226	-0.3506	-0.1605	0.3538	-0.0823	-0.1407	0.2431	0.0019	0.3605	23.7547	-34.6504	6.1351
5	0.7512	-0.3961	0.4425	1.5478	-0.5187	2.4472	0.131	0.0933	-0.1531	-0.1919	-0.0249	0.1078	0.4423	-0.0404	-0.102	0.184	0.0048	-0.0109	0.1187	-0.0154	0.144	37.6605	-33.2343	15.7334
6	1.6394	-0.2562	-0.0447	2.1004	0.1107	1.8954	-0.0302	-0.1228	-0.2357	0.1839	-0.0038	0.3333	0.3128	-0.3042	0.0014	0.1475	-0.0352	0.0292	0.1608	0.0184	0.1832	26.5487	-22.1205	21.8093
7	1.4822	0.1537	0.5088	1.649	0.1191	1.1742	-0.1063	-0.2798	0.2177	0.4144	0.0091	-0.1868	-0.1573	0.0453	0.0784	0.2627	-0.002	-0.0615	0.1775	-0.0414	0.1939	46.9817	3.4241	41.6422
8	2.9967	1.6562	-0.619	2.2521	-1.2017	1.4979	0.1169	-0.4795	0.1584	0.5631	-0.0602	0.0524	-0.1542	0.0513	-0.0714	0.2515	0.0259	-0.001	0.1944	-0.0233	0.1635	42.2129	-12.7351	43.5371
9	1.5333	0.0904	0.6332	1.6471	-0.3982	2.3647	0.0214	-0.113	-0.0517	0.3063	0.0186	-1.0393	0.0191	0.4666	0.015	0.2978	0.0913	-0.162	0.2942	-0.0179	0.475	63.9628	-32.6618	41.4665
10	0.8568	-0.3523	0.3141	1.7129	-0.0331	1.947	0.0593	-0.01	-0.0701	0.1692	-0.0144	-0.2268	0.2718	0.2381	-0.0126	0.1658	0.0386	-0.0293	0.1365	0.0106	0.1702	50.2077	-33.5085	31.499
11	2.025	0.9741	-0.6928	2.466	-0.8329	1.997	-0.0753	-0.0415	-0.0549	0.0017	-0.0316	-0.4953	0.1122	0.3655	0.1172	0.122	0.0225	-0.0166	0.1736	-0.014	0.2218	55.9703	-16.658	30.7773

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 94 )	A	15 - 94
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 192 )	A	95 - 192
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 193 through 265 )	A	193 - 265
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 15 through 79 )	B	15 - 79
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 80 through 192 )	B	80 - 192
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 193 through 265 )	B	193 - 265
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 15 through 192 )	C	15 - 192
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 193 through 265 )	C	193 - 265
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 15 through 79 )	D	15 - 79
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 80 through 192 )	D	80 - 192
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 193 through 265 )	D	193 - 265

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