PDB-4nbu: Crystal structure of FabG from Bacillus sp

ID or keywords:

Entry

Database: PDB / ID: 4nbu

Title

Crystal structure of FabG from Bacillus sp

Components

3-oxoacyl-(Acyl-carrier-protein) reductase

3-oxoacyl-(acyl-carrier-protein) reductase

Keywords

OXIDOREDUCTASE /

reductase

Function / homology

Function and homology information

oxidoreductase activity /

nucleotide binding
Similarity search - Function

Biological species

Bacillus sp. SG-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.34 Å

Authors

Pereira, J.H. / Mcandrew, R.P. / Javidpour, P. / Beller, H.R. / Adams, P.D.

Citation

Journal: Appl.Environ.Microbiol. / Year: 2014
Title: Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions.
Authors: Javidpour, P. / Pereira, J.H. / Goh, E.B. / McAndrew, R.P. / Ma, S.M. / Friedland, G.D. / Keasling, J.D. / Chhabra, S.R. / Adams, P.D. / Beller, H.R.

History

Deposition	Oct 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4nbu.cif.gz	393.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4nbu.ent.gz	324.4 KB	Display	PDB format
PDBx/mmJSON format	4nbu.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/nb/4nbu ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbu	HTTPS FTP

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Related structure data

Related structure data	4nbtC 4nbvC 4nbwC 1q7bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tox-3 3tox-2 4cqm-1 5h5x-3 4ure-1 4cql-3 2ph3-1 3uf0-1 3uf0-3 2wdz-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	#216 - Dec 2017 Biodegradable Plastic similarity (3) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

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

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	63.412, 68.774, 70.000
Angle α, β, γ (deg.)	67.85, 88.65, 62.64
Int Tables number	1
Space group name H-M	P1

#1: Protein	3-oxoacyl-(Acyl-carrier-protein) reductase / 3-oxoacyl-(acyl-carrier-protein) reductase Mass: 27040.068 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. SG-1 (bacteria) / Gene: BSG1_13201 / Production host: Escherichia coli (E. coli) / References: UniProt: A6CQL2
#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: Chemical	ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA Mass: 851.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₄₀N₇O₁₈P₃S
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.28 Å³/Da / Density % sol: 46.12 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Sodium citrate and 20% PEG 3,350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012
Radiation	Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.34→23.32 Å / Num. all: 201546 / Num. obs: 201546 / % possible obs: 93.68 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 1.34→1.3731 Å / % possible all: 93.68

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Processing

Software

Name	Version	Classification
BOS		data collection
PHENIX		model building
PHENIX	(phenix.refine: dev_1405)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q7B

1q7b

Resolution: 1.34→23.32 Å / SU ML: 0.11 / σ(F): 1.98 / Phase error: 17.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1644	2006	1 %
R_work	0.1557	-	-
obs	0.1558	201546	93.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.34→23.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7286	0	230	938	8454

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7724
X-RAY DIFFRACTION	f_angle_d	1.137	10497
X-RAY DIFFRACTION	f_dihedral_angle_d	14.902	2889
X-RAY DIFFRACTION	f_chiral_restr	0.072	1214
X-RAY DIFFRACTION	f_plane_restr	0.004	1348

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 (%)
1.34-1.3731	0.2583	110	0.2287	11873	X-RAY DIFFRACTION	78
1.3731-1.4102	0.198	133	0.2141	13164	X-RAY DIFFRACTION	86
1.4102-1.4517	0.22	148	0.2016	13814	X-RAY DIFFRACTION	91
1.4517-1.4985	0.2026	132	0.1861	14228	X-RAY DIFFRACTION	94
1.4985-1.5521	0.1857	143	0.1669	14353	X-RAY DIFFRACTION	94
1.5521-1.6142	0.1754	149	0.1533	14397	X-RAY DIFFRACTION	95
1.6142-1.6877	0.1539	152	0.1464	14456	X-RAY DIFFRACTION	95
1.6877-1.7766	0.15	150	0.1435	14490	X-RAY DIFFRACTION	96
1.7766-1.8879	0.1426	146	0.1461	14657	X-RAY DIFFRACTION	96
1.8879-2.0336	0.1642	151	0.1466	14668	X-RAY DIFFRACTION	96
2.0336-2.238	0.1777	143	0.1431	14738	X-RAY DIFFRACTION	97
2.238-2.5615	0.1379	153	0.1515	14847	X-RAY DIFFRACTION	97
2.5615-3.2259	0.1553	147	0.1558	14912	X-RAY DIFFRACTION	98
3.2259-23.3317	0.1651	149	0.1522	14943	X-RAY DIFFRACTION	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	1.3027	0.2528	0.1846	0.9545	0.1681	1.1832	0.0045	0.173	-0.086	-0.3568	0.1434	0.2745	0.3207	-0.2236	-0.0724	0.2715	-0.0701	-0.077	0.1862	0.0095	0.1805	57.1027	24.7518	56.5112
2	0.814	0.3089	0.0224	0.9326	-0.1948	1.4537	0.0043	0.0958	-0.1145	-0.1416	0.0134	0.0079	0.2183	-0.0129	-0.0218	0.1468	-0.0072	-0.0158	0.0872	-0.0108	0.1038	69.5099	24.6102	67.2127
3	2.235	-0.0941	0.1292	2.2222	0.4074	1.7138	-0.0211	-0.1504	-0.0742	0.0492	-0.0102	0.3588	0.1521	-0.2993	0.012	0.1149	-0.0302	-0.0147	0.113	0.0173	0.1346	60.0317	38.5839	69.0949
4	2.627	-0.2382	0.4065	0.9724	0.1103	2.6785	-0.0279	-0.2253	0.0111	0.3316	-0.0221	-0.0113	-0.078	-0.0302	0.0331	0.1752	-0.0455	0.002	0.1105	-0.0102	0.0765	85.5837	62.5817	100.2781
5	1.9656	0.3028	0.7464	0.6854	0.0274	1.0813	-0.0241	-0.0157	0.0876	0.0256	-0.0449	-0.0073	-0.1348	0.0498	0.0646	0.1011	-0.0137	0.0089	0.0757	0.0018	0.0606	82.3634	62.7139	83.8518
6	1.957	0.6152	-0.1104	2.0457	0.1236	2.4686	0.0878	-0.1512	0.1578	0.1991	-0.1048	0.2886	-0.1279	-0.319	-0.0032	0.1181	-0.0094	0.0243	0.1017	-0.0124	0.1062	74.3518	50.1928	92.1504
7	3.9759	-0.8904	-0.0033	3.3127	0.0036	3.7699	0.0739	-0.0844	-0.1113	0.2395	-0.0662	-0.2366	0.1901	0.1453	0.0104	0.1327	-0.005	-0.0527	0.1058	0.0408	0.1167	90.1039	26.1219	98.4131
8	7.5441	4.0641	7.1043	4.2145	4.0296	8.107	0.4059	-0.0453	-0.4901	0.2199	-0.0348	-0.2385	0.776	0.1268	-0.3744	0.2422	0.0032	-0.0457	0.1355	0.0309	0.1524	86.9941	17.7185	95.9794
9	2.0447	-1.707	0.328	4.5414	1.0116	7.7248	0.2529	-0.416	-0.5142	0.6576	-0.0927	0.1857	0.9271	-0.4218	-0.1765	0.3488	-0.0702	-0.0346	0.2122	0.0992	0.2254	77.7934	15.6604	100.0213
10	0.9747	0.0804	0.0056	1.1689	-0.0228	2.5464	0.074	-0.0585	-0.077	0.0637	-0.0463	0.0022	0.1716	-0.0152	0.0014	0.0943	-0.0127	-0.018	0.0634	0.0084	0.0867	77.2002	26.4832	84.6522
11	2.8966	0.3031	-0.3728	3.2319	0.044	3.8909	0.0239	0.3743	-0.3274	-0.2405	-0.0454	-0.4731	0.3492	0.4066	0.0168	0.1647	0.0256	-0.0114	0.1341	-0.0032	0.155	88.0895	31.6397	83.362
12	4.2103	-2.7716	-2.3217	2.2229	1.379	1.3739	0.2418	0.5511	-0.0977	-0.6066	-0.4389	-0.4115	0.2974	0.247	-0.0025	0.2702	0.0751	0.0752	0.3036	-0.008	0.2839	97.6584	37.8526	74.9919
13	3.5402	-0.444	-1.3989	2.0805	0.3664	2.8878	0.0402	-0.1386	-0.0472	0.1105	-0.0409	-0.1144	0.0155	0.1012	0.0005	0.0823	-0.0242	-0.0132	0.0358	0.0086	0.0743	83.6159	40.059	89.7547
14	1.1214	0.1673	0.6943	0.7762	-0.1058	1.3954	-0.0899	0.0819	0.1523	-0.1155	0.0202	0.1365	-0.1479	-0.0333	0.0572	0.1248	-0.0013	-0.0234	0.0848	0.0079	0.109	68.2921	62.7037	61.71
15	1.4587	-0.4809	-0.0408	2.4136	-0.1053	2.5503	0.0092	0.132	0.1439	-0.2644	-0.0133	-0.2771	-0.0373	0.3232	0.0064	0.1431	-0.022	0.0057	0.1106	0.009	0.1027	75.5827	48.7656	60.0187

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 179 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 180 through 250 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 7 through 69 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 70 through 179 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 180 through 250 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 9 through 56 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 57 through 69 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 70 through 84 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 85 through 179 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 180 through 200 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 201 through 218 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 219 through 250 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 9 through 179 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 180 through 250 )

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