PDB-5vp5: Crystal structure of a 3-oxoacyl-acyl-carrier protein reductase F...

ID or keywords:

Entry

Database: PDB / ID: 5vp5

Title

Crystal structure of a 3-oxoacyl-acyl-carrier protein reductase FabG4 from Mycobacterium smegmatis bound to NAD

Components

3-oxoacyl-acyl-carrier protein reductase FabG4

Keywords

OXIDOREDUCTASE / NIAID / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of a 3-oxoacyl-acyl-carrier protein reductase FabG4 from Mycobacterium smegmatis bound to NAD
Authors: Edwards, T.E. / Mayclin, S.J. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	May 4, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 17, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5vp5.cif.gz	178 KB	Display	PDBx/mmCIF format
PDB format	pdb5vp5.ent.gz	135.9 KB	Display	PDB format
PDBx/mmJSON format	5vp5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5vp5_validation.pdf.gz	749.1 KB	Display	wwPDB validaton report
Full document	5vp5_full_validation.pdf.gz	750.2 KB	Display
Data in XML	5vp5_validation.xml.gz	20.5 KB	Display
Data in CIF	5vp5_validation.cif.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vp/5vp5 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/5vp5	HTTPS FTP

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Related structure data

Related structure data	3u0bS S: Starting model for refinement
Similar structure data	3u0b-1 6jbn-d 7bxf-d 4nch-d 2xn2-d 3o72-1 1zhh-d 5kf9-1 2yfn-d 3v1t-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-MysmA.00010.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: 3-oxoacyl-acyl-carrier protein reductase FabG4

hetero molecules

49.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3-oxoacyl-acyl-carrier protein reductase FabG4

hetero molecules

A: 3-oxoacyl-acyl-carrier protein reductase FabG4

hetero molecules

defined by author&software
99.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.580, 60.610, 76.270
Angle α, β, γ (deg.)	90.000, 126.690, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1045- HOH

#1: Protein	3-oxoacyl-acyl-carrier protein reductase FabG4 / Oxidoreductase / short chain dehydrogenase/reductase family protein Mass: 48933.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: fabG4, MSMEG_0372, MSMEI_0365 / Production host: Escherichia coli (E. coli) References: UniProt: A0QPE7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 450 / 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: 1.92 Å³/Da / Density % sol: 36.06 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: MysmA.00010.a.A1.PW28467 at 19.87 mg/mL with 4 mM NAD against MCSG1 screen condition E3 50 mM MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 550 MME soaked overnight with 10 mM NAD, crystal tracking ID ...Details: MysmA.00010.a.A1.PW28467 at 19.87 mg/mL with 4 mM NAD against MCSG1 screen condition E3 50 mM MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 550 MME soaked overnight with 10 mM NAD, crystal tracking ID 271652e3, unique puck ID hnk3-3

Crystal

Density Matthews: 1.92 Å³/Da / Density % sol: 36.06 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop
Details: MysmA.00010.a.A1.PW28467 at 19.87 mg/mL with 4 mM NAD against MCSG1 screen condition E3 50 mM MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 550 MME soaked overnight with 10 mM NAD, crystal tracking ID ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.8→48.625 Å / Num. obs: 34407 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.336 % / B_iso Wilson estimate: 14.97 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.035 / R_rim(I) all: 0.042 / Χ²: 1.008 / Net I/σ(I): 22.99

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.85	2.955	0.127	7.42	2513	0.975	0.155	98.4
1.85-1.9	3.44	0.101	10.47	2471	0.986	0.12	99.8
1.9-1.95	3.476	0.089	12.12	2409	0.99	0.105	99.7
1.95-2.01	3.42	0.076	13.83	2330	0.992	0.09	99.5
2.01-2.08	3.296	0.067	15.61	2272	0.993	0.081	99.5
2.08-2.15	3.22	0.057	17.81	2174	0.995	0.068	99.5
2.15-2.23	3.487	0.054	19.45	2122	0.996	0.064	99.3
2.23-2.32	3.46	0.047	21.71	2032	0.997	0.056	99.4
2.32-2.43	3.393	0.045	22.78	1964	0.997	0.054	99.4
2.43-2.55	3.206	0.042	24.02	1866	0.997	0.051	99.1
2.55-2.68	3.352	0.038	26.9	1781	0.997	0.045	98.9
2.68-2.85	3.455	0.034	29.41	1674	0.998	0.041	99.3
2.85-3.04	3.417	0.031	32.32	1586	0.998	0.037	98.9
3.04-3.29	3.202	0.029	33.74	1476	0.998	0.035	98.7
3.29-3.6	3.32	0.025	39.15	1366	0.999	0.03	99.2
3.6-4.02	3.449	0.023	41.15	1226	0.999	0.027	98.5
4.02-4.65	3.303	0.022	42.5	1093	0.999	0.026	98.9
4.65-5.69	3.236	0.023	41.01	920	0.999	0.028	98.3
5.69-8.05	3.372	0.025	42.4	717	0.998	0.03	97.6
8.05-48.625	3.113	0.025	46.01	415	0.999	0.03	96.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	(dev_2744)	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3U0B

3u0b

Resolution: 1.8→48.625 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 15.82

	R_factor	Num. reflection	% reflection
R_free	0.177	2086	6.06 %
R_work	0.1355	-	-
obs	0.1379	34404	99.54 %

Solvent computation

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

Displacement parameters

B_iso max: 72.58 Å² / B_iso mean: 18.2766 Å² / B_iso min: 6.31 Å²

Refinement step

Cycle: final / Resolution: 1.8→48.625 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2954	0	46	451	3451
B_iso mean	-	-	17.56	29.23	-
Num. residues	-	-	-	-	411

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3111
X-RAY DIFFRACTION	f_angle_d	0.791	4266
X-RAY DIFFRACTION	f_chiral_restr	0.057	513
X-RAY DIFFRACTION	f_plane_restr	0.005	582
X-RAY DIFFRACTION	f_dihedral_angle_d	10.775	1888

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 (%)
1.7999-1.8418	0.2068	157	0.1619	2105	2262	98
1.8418-1.8879	0.2301	152	0.1535	2120	2272	100
1.8879-1.9389	0.2035	145	0.1445	2127	2272	100
1.9389-1.996	0.1866	117	0.1446	2176	2293	100
1.996-2.0604	0.2009	136	0.141	2152	2288	100
2.0604-2.1341	0.2036	130	0.1432	2179	2309	100
2.1341-2.2195	0.1886	131	0.1401	2151	2282	100
2.2195-2.3205	0.1606	130	0.135	2156	2286	100
2.3205-2.4428	0.2027	175	0.1368	2120	2295	100
2.4428-2.5959	0.172	149	0.1367	2131	2280	100
2.5959-2.7963	0.1543	139	0.1342	2162	2301	100
2.7963-3.0777	0.1785	166	0.1318	2124	2290	100
3.0777-3.5229	0.154	122	0.1283	2185	2307	100
3.5229-4.438	0.1541	108	0.1155	2210	2318	99
4.438-48.6424	0.1669	129	0.1431	2220	2349	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	2.4072	-0.7226	0.086	2.4764	-0.9766	0.9573	0.0372	0.1475	0.0173	-0.1674	-0.0759	-0.1231	0.0055	0.0572	0.0445	0.1407	-0.0188	0.0247	0.142	-0.0232	0.0768	19.0271	10.1608	-22.4505
2	0.6581	0.0066	0.2643	0.7928	-0.1847	1.4296	0.0045	-0.0092	0.0008	0.0122	0.0025	-0.0296	-0.0381	0.1113	-0.0056	0.0684	-0.0064	0.0165	0.0931	-0.0068	0.0732	14.1876	5.6075	-10.8026
3	5.6914	-1.7525	0.2143	2.1122	0.0002	1.2362	-0.0138	0.2259	0.1235	-0.0515	0.0183	-0.0719	-0.0884	0.0374	-0.0275	0.1039	-0.0271	-0.0035	0.0816	0.014	0.046	-8.0311	8.205	-28.215
4	1.5875	1.4423	-2.5313	2.8988	-3.3033	4.9893	-0.023	0.1507	0.2971	0.0068	0.2475	0.2	-0.1233	-0.3244	-0.2443	0.0848	-0.0001	-0.0307	0.1406	0.0186	0.1148	-21.0463	10.3885	-28.5682
5	0.6069	-0.0427	-0.1106	1.3026	1.6719	3.5898	0.0223	-0.0528	0.0565	-0.0465	-0.033	0.0749	-0.1757	-0.2514	0.0797	0.0857	0.0149	-0.0125	0.0828	0.0215	0.1028	-20.6518	7.3353	-16.0718
6	0.7072	0.3693	0.2238	1.3601	1.4701	3.0296	-0.0026	-0.0372	0.0071	0.0402	0.0617	-0.036	-0.0122	0.0373	-0.0695	0.0805	0.0153	-0.0098	0.0791	0.0186	0.0945	-12.8927	3.1079	-13.6758
7	1.9806	0.0165	-0.2333	0.1434	0.1211	2.119	0.0356	0.0503	0.2326	0.0052	-0.0382	-0.0871	-0.2493	0.033	-0.0558	0.1127	0.0028	-0.0124	0.0974	0.0116	0.1172	-6.753	8.9136	-11.2618
8	2.459	0.2427	0.2752	3.3102	-0.1503	1.6766	-0.0148	-0.1815	0.1426	0.2188	-0.0294	0.0061	-0.1384	0.088	0.0175	0.0772	-0.0247	0.0004	0.1036	-0.0123	0.0708	-0.101	7.9097	-15.2742

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 26 through 78 )	A	26 - 78
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 202 )	A	79 - 202
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 203 through 241 )	A	203 - 241
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 242 through 268 )	A	242 - 268
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 269 through 316 )	A	269 - 316
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 317 through 353 )	A	317 - 353
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 354 through 416 )	A	354 - 416
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 417 through 450 )	A	417 - 450

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