PDB-4nbt: Crystal structure of FabG from Acholeplasma laidlawii

ID or keywords:

Entry

Database: PDB / ID: 4nbt

Title

Crystal structure of FabG from Acholeplasma laidlawii

Components

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

Keywords

OXIDOREDUCTASE / reductase

Function / homology

Function and homology information

3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / nucleotide binding
Similarity search - Function

Biological species

Acholeplasma laidlawii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 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	Dec 10, 2014	Group: Other
Revision 1.3	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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Download

PDBx/mmCIF format	4nbt.cif.gz	536.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4nbt.ent.gz	453.4 KB	Display	PDB format
PDBx/mmJSON format	4nbt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nbt_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	4nbt_full_validation.pdf.gz	1.6 MB	Display
Data in XML	4nbt_validation.xml.gz	49 KB	Display
Data in CIF	4nbt_validation.cif.gz	73.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbt ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbt	HTTPS FTP

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Related structure data

Related structure data	4nbuC 4nbvC 4nbwC 1q7bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ovj-1 4ni5-1 5aup-d 4jf9-1 3zv3-1 4nbu-d 4cqm-2 5ltq-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 (4) #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

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

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

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

hetero molecules

105 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)	61.968, 62.364, 66.765
Angle α, β, γ (deg.)	66.03, 76.63, 79.93
Int Tables number	1
Space group name H-M	P1

#1: Protein	3-oxoacyl-[acyl-carrier-protein] reductase Mass: 25532.424 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acholeplasma laidlawii (bacteria) / Strain: PG-8A / Gene: fabG2, ACL_0504 / Production host: Escherichia coli (E. coli) References: UniProt: A9NFJ2, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1296 / 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: 2.24 Å³/Da / Density % sol: 45.01 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Ammonium fluoride and 20% PEG 3,350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / 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: 1.48→39.487 Å / Num. obs: 142273 / % possible obs: 96.43 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Highest resolution: 1.48 Å / % possible all: 96.43

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Processing

Software

Name	Version	Classification
BOS		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.2_1309)	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: 1.48→39.487 Å / SU ML: 0.11 / σ(F): 1.97 / Phase error: 14.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.154	2000	1.41 %
R_work	0.1282	-	-
obs	0.1285	142258	96.43 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.48→39.487 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7132	0	176	1296	8604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7420
X-RAY DIFFRACTION	f_angle_d	1.385	10084
X-RAY DIFFRACTION	f_dihedral_angle_d	13.526	2676
X-RAY DIFFRACTION	f_chiral_restr	0.095	1196
X-RAY DIFFRACTION	f_plane_restr	0.006	1264

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 (%)
1.4801-1.5171	0.1803	138	0.1735	9651	X-RAY DIFFRACTION	93
1.5171-1.5581	0.1857	141	0.1546	9859	X-RAY DIFFRACTION	95
1.5581-1.6039	0.2033	139	0.1481	9820	X-RAY DIFFRACTION	95
1.6039-1.6557	0.1818	141	0.1373	9877	X-RAY DIFFRACTION	95
1.6557-1.7149	0.1544	143	0.1302	9989	X-RAY DIFFRACTION	96
1.7149-1.7836	0.1699	141	0.1285	9938	X-RAY DIFFRACTION	96
1.7836-1.8647	0.1614	143	0.1249	9994	X-RAY DIFFRACTION	96
1.8647-1.963	0.1695	142	0.1242	10030	X-RAY DIFFRACTION	97
1.963-2.086	0.1454	144	0.118	10096	X-RAY DIFFRACTION	97
2.086-2.2471	0.1372	145	0.1121	10096	X-RAY DIFFRACTION	97
2.2471-2.4732	0.1332	145	0.1155	10212	X-RAY DIFFRACTION	98
2.4732-2.831	0.1469	146	0.1293	10167	X-RAY DIFFRACTION	98
2.831-3.5663	0.1431	145	0.1302	10232	X-RAY DIFFRACTION	99
3.5663-39.5009	0.1568	147	0.1305	10297	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	0.0475	0.0119	-0.0041	0.0325	-0.0273	0.0194	0.0612	0.0196	-0.0052	0.054	-0.0377	0.1	0.0229	-0.114	0	0.1098	0.0228	-0.0049	0.0989	-0.0082	0.0986	-20.7188	-41.8215	44.0451
2	0.1436	-0.0571	-0.0047	0.1364	0.0721	0.0895	0.0318	0.0894	0.0386	-0.1003	-0.075	0.0772	-0.1271	-0.1488	-0.0057	0.1261	0.0443	-0.0252	0.1082	0.0058	0.1116	-20.7242	-39.4797	35.8232
3	0.1362	-0.01	0.0822	0.0935	-0.0739	0.0744	0.0354	0.0683	-0.0088	-0.1264	-0.0436	0.0313	-0.0806	-0.0559	0.0012	0.1135	0.0162	-0.0233	0.0847	-0.0076	0.084	-10.9039	-52.7562	30.1641
4	0.1801	-0.0837	-0.0719	0.1152	0.0301	0.0631	0.0123	0.0151	0.0356	-0.0544	-0.0132	-0.0068	-0.0256	0.0047	0.0067	0.0913	0.0034	-0.0093	0.0528	0.0066	0.064	-5.7032	-48.3935	37.5562
5	0.2366	-0.0658	-0.0487	0.1912	-0.1486	0.1398	0.0568	0.1106	-0.0141	-0.2551	-0.0991	0.2234	-0.0005	-0.0461	0.0011	0.1419	0.0214	-0.06	0.1133	-0.024	0.1185	-20.8016	-63.399	39.7205
6	0.0446	0.0125	0.0149	0.05	-0.0497	0.0526	-0.0322	-0.024	-0.0196	-0.024	0.0263	0.0231	-0.0051	0.0119	-0.0001	0.0727	0.004	-0.0047	0.0794	-0.0057	0.0693	-10.0071	-56.1178	48.9223
7	0.0664	-0.0062	-0.0625	0.098	0.0381	0.0615	0.0341	-0.0857	0.0794	0.1223	-0.0183	0.0771	-0.1243	-0.0435	0.0014	0.0963	0.0089	0.0229	0.1188	-0.0263	0.0923	-18.5072	-56.5629	71.3251
8	0.0249	0.0131	0.0069	0.0254	0.0024	0.0643	-0.0596	-0.1333	-0.0765	0.1394	0.009	0.0475	0.0653	-0.0359	-0.0022	0.1101	-0.0038	0.0379	0.1494	0.0106	0.0936	-17.4982	-70.2841	76.4024
9	0.028	-0.0461	-0.0699	0.0872	0.1117	0.1371	-0.0839	-0.0875	0.0109	0.0859	0.0554	0.0145	-0.0248	0.0035	0.0001	0.0662	-0.013	0.0028	0.0984	-0.0105	0.0692	-1.2175	-64.9851	68.9086
10	0.1403	-0.0934	-0.0141	0.1776	0.0482	0.1171	-0.0083	-0.031	-0.0435	0.0324	-0.0019	0.0246	0.0084	-0.0048	-0.0079	0.0592	-0.0079	0.0009	0.0797	0.0061	0.0659	-6.4312	-69.3963	62.5705
11	0.1222	-0.065	-0.0927	0.2052	-0.0646	0.1617	0.0022	-0.1199	-0.0106	0.0656	-0.0276	-0.0695	-0.0377	0.0534	-0.0041	0.0788	-0.0137	-0.0152	0.1084	-0.0017	0.0756	-0.5527	-50.4789	62.8199
12	0.0411	0.0141	-0.0091	0.1139	-0.0221	0.0368	0.0599	0.003	0.0023	0.0093	-0.0547	0.005	-0.019	-0.0199	0.0009	0.0618	-0.0007	0.0013	0.0744	-0.0059	0.0696	-10.6282	-55.6084	56.0163
13	0.0278	-0.014	0.01	0.0601	0.0438	0.0462	-0.0029	0.0138	-0.0227	-0.0583	0.0046	-0.0224	0.0792	0.0766	0.0009	0.0718	0.018	0.0119	0.0899	0.0043	0.0977	21.5183	-83.458	48.5638
14	0.0147	-0.0063	0.0127	0.0071	0.0005	0.0191	-0.0271	0.0121	-0.0845	0.0039	0.0336	-0.07	0.145	0.0546	-0	0.097	0.0117	0.0078	0.0864	0.0026	0.1345	21.7846	-90.1793	53.3807
15	0.0324	0.0281	-0.0014	0.0333	-0.0132	0.0133	-0.0502	-0.1376	-0.0227	0.0832	0.0421	-0.0498	0.0915	0.1059	-0.0001	0.0862	0.0184	-0.0154	0.1294	0.0113	0.1077	22.018	-84.3634	64.9798
16	0.0661	-0.1078	0.0116	0.1557	-0.0349	0.0648	-0.0522	-0.0791	-0.0462	-0.0045	0.0216	0.0249	0.0673	0.0152	-0.0002	0.054	-0.0068	-0.0034	0.0641	0.0034	0.0935	4.7308	-81.2037	58.7525
17	0.0999	-0.0696	-0.0179	0.0893	0.1064	0.1388	-0.0108	-0.0374	0.013	0.0139	0.0207	-0.0084	0.0115	0.0204	0.0125	0.0557	-0.0045	-0.0054	0.0725	0.0076	0.0767	9.5436	-73.1964	59.1408
18	0.1868	-0.1078	0.0712	0.1393	0.0264	0.1874	0.021	0.0302	-0.065	-0.0242	0.0062	-0.0114	0.046	0.0161	0.0032	0.0673	-0.0057	-0.0068	0.0599	0.0033	0.0844	6.5763	-78.3372	44.2192
19	0.2078	-0.1191	0.0231	0.326	0.1159	0.3365	0.0276	0.0394	0.0149	-0.1101	-0.0108	-0.0479	-0.04	0.0387	-0.0018	0.0993	-0.0062	0.0277	0.0671	0.0051	0.0607	11.4849	-60.1846	25.0766
20	0.2378	-0.1458	-0.0176	0.107	-0.07	0.4408	-0.0138	0.0072	0.0091	-0.0482	0.0366	-0.0699	-0.0908	0.0635	0.0012	0.0787	-0.0137	0.011	0.071	-0.0024	0.0771	14.7951	-61.0961	39.1133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 94 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 178 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 179 through 220 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 221 through 240 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 47 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 72 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 73 through 94 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 95 through 168 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 169 through 208 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 209 through 240 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 29 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 30 through 47 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 48 through 72 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 73 through 94 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 95 through 168 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 169 through 240 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 2 through 163 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 164 through 240 )

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