PDB-4nbw: Crystal structure of FabG from Plesiocystis pacifica

ID or keywords:

Entry

Database: PDB / ID: 4nbw

Title

Crystal structure of FabG from Plesiocystis pacifica

Components

Short-chain dehydrogenase/reductase SDR

Keywords

OXIDOREDUCTASE / reductase

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Plesiocystis pacifica SIR-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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_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	4nbw.cif.gz	543.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4nbw.ent.gz	459.6 KB	Display	PDB format
PDBx/mmJSON format	4nbw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nbw_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4nbw_full_validation.pdf.gz	1.6 MB	Display
Data in XML	4nbw_validation.xml.gz	50.1 KB	Display
Data in CIF	4nbw_validation.cif.gz	71.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbw ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbw	HTTPS FTP

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Related structure data

Related structure data	4nbtC 4nbuC 4nbvC 1q7bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1zem-2 5ics-d 6pei-d 2ztl-d 4e6p-d 3wds-d 3svt-1 2uvd-2 4trr-2 5icm-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	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

A: Short-chain dehydrogenase/reductase SDR

B: Short-chain dehydrogenase/reductase SDR

C: Short-chain dehydrogenase/reductase SDR

D: Short-chain dehydrogenase/reductase SDR

hetero molecules

109 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)	77.730, 75.140, 97.725
Angle α, β, γ (deg.)	90.00, 113.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Short-chain dehydrogenase/reductase SDR Mass: 26632.430 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plesiocystis pacifica SIR-1 (bacteria) / Gene: PPSIR1_02236 / Production host: Escherichia coli (E. coli) / References: UniProt: A6G411
#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.: 928 / 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: 2.46 Å³/Da / Density % sol: 49.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Ammonium tartrate dibasic pH 7.0 and 25 % PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / 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: 2→44.832 Å / Num. all: 61472 / Num. obs: 61472 / % possible obs: 87.91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2→2.0501 Å / % possible all: 87.91

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Processing

Software

Name	Version	Classification
BOS		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.3_1479)	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: 2→44.832 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 23.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2457	1994	3.24 %
R_work	0.2046	-	-
obs	0.206	61472	87.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→44.832 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7360	0	176	928	8464

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	7656
X-RAY DIFFRACTION	f_angle_d	1.334	10416
X-RAY DIFFRACTION	f_dihedral_angle_d	15.497	2680
X-RAY DIFFRACTION	f_chiral_restr	0.099	1228
X-RAY DIFFRACTION	f_plane_restr	0.007	1332

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 (%)
2-2.0501	0.2933	139	0.2572	4174	X-RAY DIFFRACTION	87
2.0501-2.1055	0.2644	142	0.2482	4210	X-RAY DIFFRACTION	87
2.1055-2.1674	0.2896	146	0.2319	4248	X-RAY DIFFRACTION	88
2.1674-2.2374	0.2566	141	0.2242	4203	X-RAY DIFFRACTION	88
2.2374-2.3174	0.2398	138	0.2109	4252	X-RAY DIFFRACTION	89
2.3174-2.4101	0.2649	139	0.2108	4305	X-RAY DIFFRACTION	89
2.4101-2.5198	0.2697	145	0.2129	4364	X-RAY DIFFRACTION	90
2.5198-2.6527	0.2709	149	0.2074	4340	X-RAY DIFFRACTION	91
2.6527-2.8188	0.2348	146	0.2023	4352	X-RAY DIFFRACTION	90
2.8188-3.0364	0.2118	148	0.2002	4340	X-RAY DIFFRACTION	89
3.0364-3.3419	0.2363	147	0.1834	4238	X-RAY DIFFRACTION	88
3.3419-3.8253	0.2044	134	0.1712	4115	X-RAY DIFFRACTION	85
3.8253-4.8185	0.2108	141	0.1716	4171	X-RAY DIFFRACTION	86
4.8185-44.8437	0.2786	139	0.2191	4166	X-RAY DIFFRACTION	84

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	0.5256	-0.1375	-0.0559	0.5276	0.0679	0.6918	0.007	-0.0497	0.094	0.0529	-0.0015	-0.0753	-0.096	0.1035	-0.0234	0.1012	-0.0203	0.0004	0.1132	-0.0113	0.1191	27.6462	59.3469	85.3079
2	0.1429	0.2127	-0.1137	0.6736	-0.4019	1.586	0.1105	-0.0453	0.0966	0.0645	-0.0468	-0.0324	-0.2986	0.2121	0.0028	0.1117	-0.0196	0.0281	0.1021	-0.0135	0.1208	17.8357	65.7999	75.1741
3	0.5786	-0.3702	-0.1094	0.7331	0.4386	0.969	-0.0221	-0.056	-0.0464	0.0249	-0.0352	0.0596	-0.0449	-0.1442	0.0398	0.1156	0.007	0.027	0.1177	-0.0036	0.1036	-12.7925	64.0165	80.5513
4	0.3652	-0.1948	0.133	1.0462	0.4969	0.5264	-0.0858	-0.0233	0.0109	0.1839	0.1257	0.1221	0.1224	-0.301	0.1055	0.0382	0.0411	0.0321	0.1376	0.0033	0.1286	-11.2287	61.7067	69.9868
5	1.0568	0.3095	0.0483	2.7356	0.0349	1.104	-0.1878	-0.0287	-0.8476	-0.0484	-0.0368	0.0715	0.3984	0.1158	-0.0226	0.241	-0.0417	0.1268	0.155	0.0017	0.458	-9.543	26.8794	66.4808
6	0.2538	-0.1345	0.0911	0.6388	0.246	0.4959	-0.0164	0.048	-0.0293	0.0883	-0.0082	0.0754	0.013	-0.0508	-0.0014	0.1142	-0.0077	0.0404	0.1099	-0.0062	0.1071	-1.8835	56.1696	66.595
7	0.4531	-0.7445	0.405	1.2478	-0.6196	1.2655	-0.0764	0.0438	-0.119	-0.0106	0.248	0.3751	0.1831	-0.3209	0.1998	0.1996	0.0022	0.0492	0.1041	-0.0009	0.1535	-2.9181	50.7221	80.2391
8	0.446	-0.0405	0.1605	0.8979	-0.2902	0.4891	-0.042	-0.0649	-0.0079	-0.0266	0.033	0.029	0.1547	-0.1002	-0.0266	0.2078	0.0206	0.0476	0.09	-0.0201	0.1096	3.8485	52.5697	83.3214
9	0.8391	0.2359	-0.2213	0.825	0.03	0.9318	0.1305	0.0939	-0.2634	0.1435	-0.0943	0.0267	0.2391	0.0895	0.0219	0.1357	0.0437	-0.0009	0.1212	-0.0149	0.1676	37.7471	26.8306	61.2684
10	0.4728	-0.1411	-0.224	1.0343	0.7739	0.9379	-0.0246	0.0589	-0.1013	0.2402	0.0288	-0.1022	-0.0881	0.1075	-0.1181	0.0187	0.0074	0.0037	0.1783	-0.0128	0.1835	43.8839	31.5139	65.2344
11	0.6413	0.0848	-0.1403	0.4552	0.0181	0.1756	0.0456	-0.066	-0.0294	0.1805	-0.0756	-0.1164	0.1034	0.2602	0.0339	-0.0918	0.0612	-0.0316	0.1505	0.0373	0.175	40.2552	38.0873	65.942
12	1.086	-0.0269	-0.8366	0.9679	0.0589	1.8369	0.0962	-0.3352	-0.1055	0.1965	-0.0226	0.0344	0.118	0.1929	0.0333	0.1437	0.0016	-0.0142	0.2122	0.02	0.1518	31.0492	42.173	89.8297
13	0.5739	-0.0216	0.0481	0.3292	0.0043	0.4376	-0.0256	0.0197	0.0101	0.0633	0.014	-0.0402	0	0.0415	-0.0073	0.111	0.0078	0.0058	0.0689	-0.0074	0.0983	30.6468	45.0519	65.7047
14	0.6362	0.1699	-0.527	0.7311	0.3824	0.9002	-0.0421	-0.2727	-0.1481	0.5803	-0.3458	-0.0355	0.4086	0.3031	0.0153	-0.0575	0.1323	-0.0479	0.1941	0.0719	0.0711	25.4695	31.1739	71.0033
15	1.3393	0.1016	-0.0008	0.5527	0.0238	1.859	-0.1128	-0.1935	-0.069	-0.0092	-0.1023	-0.1374	0.4465	0.1441	0.0315	0.2485	0.0159	0.0375	0.1232	0.0149	0.1107	14.6003	24.3555	76.6473
16	0.3964	-0.3923	0.5938	0.5086	-0.4844	2.8365	0.1771	0.1348	-0.0719	-0.047	0.1218	-0.0114	0.2537	0.0098	0.1272	0.0761	0.0264	0.0086	0.1054	-0.0419	0.1296	24.7126	30.96	59.8206
17	0.5439	0.144	-0.0732	0.5175	-0.1203	0.6504	0.1669	0.0556	-0.0327	-0.0017	-0.0693	-0.0151	-0.0425	0.0162	0.2357	0.031	0.0226	0.0132	0.103	0.0065	0.1043	20.1776	38.7441	60.5065
18	0.8055	0.2025	-0.1257	2.0763	-0.2906	0.9561	-0.0165	0.1679	-0.0889	0.065	0.0452	-0.1027	-0.1235	-0.0252	0.0212	0.0817	0.0005	-0.0202	0.096	-0.0127	0.0808	8.1122	33.039	44.4362
19	0.8976	-0.1065	-0.5823	0.3089	0.4799	0.9742	0.1025	0.09	0.0135	-0.2522	-0.0669	-0.0153	-0.1694	-0.1448	0.0251	0.1351	0.0038	-0.0114	0.1257	-0.0208	0.1249	1.5595	33.0763	40.0099
20	0.2806	-0.3509	-0.0917	1.4263	0.2843	0.5691	0.0127	0.069	-0.0461	-0.2127	0.0192	0.2021	-0.1162	-0.1685	0.016	0.1532	-0.0077	0.0155	0.1382	-0.006	0.1141	-2.5931	35.446	50.0545
21	1.0039	-0.1009	-0.0176	2.2329	-0.5602	1.2082	-0.0777	-0.2486	0.5938	0.128	-0.0428	0.0438	-0.799	-0.0879	-0.0218	0.4911	0.0337	-0.0317	0.2218	0.0001	0.2982	-3.8322	70.4888	53.7308
22	2.0127	-0.9983	0.569	2.3095	-0.1419	1.9064	0.0432	0.0311	0.2678	-0.3853	-0.1024	0.0933	-0.0918	-0.0968	-0.0171	0.1325	0.0298	-0.024	0.1505	-0.0002	0.1205	-5.9135	51.2055	54.3849
23	0.2467	-0.0241	-0.0653	0.325	0.312	0.4292	0.0093	-0.016	0.0125	-0.0679	0.007	-0.0033	-0.0922	-0.1254	0.0056	0.1349	0.008	0.021	0.0859	-0.0071	0.1194	2.765	38.8569	60.1552
24	0.6819	0.9131	-0.6639	2.3539	-1.2863	1.3511	-0.1459	0.3057	0.2255	-0.2742	0.2811	0.1327	0.0257	-0.2363	-0.1448	0.2811	-0.0541	-0.0009	0.0566	0.0168	0.1773	10.547	46.4508	49.0232
25	0.4732	0.3637	-0.372	0.7679	-0.3243	0.5018	0.0221	0.104	0.0804	-0.2929	0.0681	0.0267	-0.0599	0.0327	-0.0397	0.1949	-0.0109	0.0046	0.1147	0.0034	0.1138	18.5145	48.5903	47.5816
26	0.3175	0.184	-0.1354	0.8489	-0.064	0.5131	0.0835	0.0678	0.0171	-0.0041	-0.0811	0.1725	-0.2246	-0.1093	-0.0013	0.1204	-0.0193	0.0082	0.0846	-0.0121	0.1526	15.8323	38.1727	58.8554

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 191 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 192 through 262 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 12 through 72 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 73 through 105 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 106 through 118 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 119 through 191 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 192 through 212 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 213 through 262 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 12 through 59 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 60 through 72 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 73 through 105 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 106 through 130 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 131 through 191 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 192 through 212 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 213 through 230 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 231 through 242 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 243 through 262 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 12 through 34 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 35 through 72 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 73 through 105 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 106 through 118 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 119 through 130 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 131 through 191 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 192 through 212 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 213 through 241 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 242 through 262 )

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