PDB-4cw5: Crystal structure of the enoyl reductase domain of DfnA from Baci...

ID or keywords:

Entry

Database: PDB / ID: 4cw5

Title

Crystal structure of the enoyl reductase domain of DfnA from Bacillus amyloliquefaciens

Components

DFNA

Keywords

OXIDOREDUCTASE / TRANS-AT PKS / POLYKETIDE

Function / homology

Function and homology information

nitronate monooxygenase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / nucleotide binding
Similarity search - Function

Biological species

BACILLUS AMYLOLIQUEFACIENS FZB42 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Jakob, R.P. / Buhkari, H.S.T. / Maier, T.

Citation

Journal: Structure / Year: 2014
Title: Evolutionary Origins of the Multienzyme Architecture of Giant Fungal Fatty Acid Synthase.
Authors: Bukhari, H.S. / Jakob, R.P. / Maier, T.

History

Deposition	Apr 1, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4cw5.cif.gz	508.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4cw5.ent.gz	432.7 KB	Display	PDB format
PDBx/mmJSON format	4cw5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4cw5_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4cw5_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4cw5_validation.xml.gz	31.8 KB	Display
Data in CIF	4cw5_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cw/4cw5 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/4cw5	HTTPS FTP

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Related structure data

Related structure data	4cw4C 2z6iS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1fe2-1 1diy-1 1igx-1 3qh0-d 6kr4-4 2oyu-1 5uao-1 6ddb-d 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	#239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

A: DFNA

B: DFNA

hetero molecules

103 kDa, 2 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)	80.850, 94.000, 144.530
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DFNA Mass: 51083.281 Da / Num. of mol.: 2 / Fragment: ENOYL REDUCTASE, RESIDUES 301-752 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS FZB42 (bacteria) Description: DSM 23117 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PRIL / References: UniProt: A7Z6E3
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.74 Å³/Da / Density % sol: 55.08 % / Description: NONE
Crystal grow	Details: 15 % PEG3350, 0.1 M SODIUM MALONATE, BIS TRIS PH 6.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0003
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0003 Å / Relative weight: 1
Reflection	Resolution: 2.25→47 Å / Num. obs: 49619 / % possible obs: 99.9 % / Observed criterion σ(I): 1.68 / Redundancy: 6.6 % / R_merge(I) obs: 0.08 / Net I/σ(I): 18.3
Reflection shell	Resolution: 2.25→2.38 Å / Redundancy: 6.5 % / R_merge(I) obs: 1.23 / Mean I/σ(I) obs: 1.68 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z6I

2z6i

Resolution: 2.3→47 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 23.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2309	2504	5.1 %
R_work	0.204	-	-
obs	0.2053	49619	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6797	0	62	98	6957

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6989
X-RAY DIFFRACTION	f_angle_d	0.84	9410
X-RAY DIFFRACTION	f_dihedral_angle_d	15.176	2631
X-RAY DIFFRACTION	f_chiral_restr	0.031	1022
X-RAY DIFFRACTION	f_plane_restr	0.004	1212

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 (%)
2.3-2.3442	0.3353	134	0.2922	2552	X-RAY DIFFRACTION	100
2.3442-2.3921	0.3529	149	0.2912	2557	X-RAY DIFFRACTION	100
2.3921-2.4441	0.3117	135	0.2779	2590	X-RAY DIFFRACTION	100
2.4441-2.5009	0.2686	150	0.2688	2567	X-RAY DIFFRACTION	100
2.5009-2.5635	0.2734	148	0.262	2570	X-RAY DIFFRACTION	100
2.5635-2.6328	0.2969	148	0.2379	2602	X-RAY DIFFRACTION	100
2.6328-2.7103	0.2767	148	0.235	2574	X-RAY DIFFRACTION	100
2.7103-2.7977	0.2498	132	0.2418	2607	X-RAY DIFFRACTION	100
2.7977-2.8977	0.2526	154	0.2395	2574	X-RAY DIFFRACTION	100
2.8977-3.0137	0.2897	145	0.2394	2606	X-RAY DIFFRACTION	100
3.0137-3.1508	0.2447	130	0.2422	2607	X-RAY DIFFRACTION	100
3.1508-3.3169	0.2597	133	0.2288	2610	X-RAY DIFFRACTION	100
3.3169-3.5247	0.2762	142	0.2228	2649	X-RAY DIFFRACTION	100
3.5247-3.7967	0.2018	133	0.1995	2603	X-RAY DIFFRACTION	100
3.7967-4.1786	0.2278	116	0.1816	2660	X-RAY DIFFRACTION	100
4.1786-4.7827	0.1894	127	0.1572	2687	X-RAY DIFFRACTION	100
4.7827-6.0237	0.1798	148	0.1654	2682	X-RAY DIFFRACTION	100
6.0237-47.0098	0.1839	132	0.1755	2818	X-RAY DIFFRACTION	100

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	0.2289	-0.256	0.2178	0.3463	-0.3516	0.3648	-0.248	-0.0499	0.0247	0.1346	0.3246	0.1637	0.0383	0.1251	0.0001	0.4589	-0.0225	0.0533	0.4136	-0.0096	0.4196	40.3903	51.0315	47.3501
2	0.134	-0.1064	0.0927	0.0907	-0.0674	0.0615	-0.1948	-0.1913	0.1097	0.2928	0.2848	0.4253	-0.2122	0.0874	-0	0.6969	0.059	0.0992	0.4809	0.0162	0.4793	38.2211	66.0363	59.0078
3	0.1791	-0.1077	0.0304	0.2509	-0.1852	0.1382	-0.1436	-0.019	-0.0174	0.6738	0.3712	0.0839	0.1234	-0.1173	0.0024	0.7578	0.1372	0.0224	0.4862	-0.0402	0.3385	41.9576	63.6685	65.6407
4	0.822	-0.6192	-0.5566	0.9582	0.1845	0.4575	-0.0759	0.0076	0.2948	0.9367	0.4488	-0.2803	0.1736	0.1604	0.0715	0.72	0.092	-0.1985	0.5362	-0.1746	0.6032	53.1581	61.7732	63.8538
5	0.1534	0.0253	-0.0789	0.002	-0.0092	0.0681	-0.05	-0.0167	-0.8449	1.0251	0.0646	-0.1937	-0.7832	-0.6686	-0.0037	0.9108	0.2983	-0.24	0.8685	-0.0344	0.9468	56.9141	42.3967	62.2655
6	0.1153	-0.4903	0.3251	2.1188	-1.4152	0.986	-0.0773	0.1033	-0.4921	0.4312	0.4433	-1.1118	-0.282	0.3125	0.1911	0.3327	-0.0208	-0.0098	0.552	-0.245	0.9388	60.5733	59.8246	51.607
7	0.0323	0.0153	-0.0092	0.0167	-0.0047	0.0022	-0.1123	-0.3306	-0.0071	0.4441	-0.2409	0.0359	-0.0851	0.1651	0.0004	0.9149	0.2055	-0.4001	1.0722	0.0365	1.9749	71.0443	55.4609	66.8674
8	0.3056	-0.3869	-0.1137	0.5978	-0.2606	1.4466	0.1825	0.1145	-0.33	0.2203	0.4816	-0.5999	-0.1646	0.0322	0.4024	0.5386	0.1088	-0.3123	0.5788	-0.1844	0.9032	61.1957	53.1356	59.7929
9	0.3638	0.5464	0.1775	0.8085	0.2675	0.0907	0.0035	0.2027	-0.0811	-0.4718	0.8124	-0.7075	-0.1056	0.3129	0.1859	0.4835	0.0655	0.2095	0.7355	-0.179	1.0835	60.8777	53.3888	43.0614
10	0.2705	0.0128	-0.0932	0.5856	-0.2754	0.1903	-0.0068	-0.0168	-0.0415	0.0565	0.2272	-0.011	-0.3021	0.0892	0	0.5313	-0.0102	0.1231	0.3759	-0.0268	0.409	41.3078	69.5788	45.8216
11	0.0542	0.036	0.1784	0.0205	0.1197	0.401	0.0435	0.4721	-0.2332	-0.0271	0.0438	-0.3791	-0.2243	0.2625	-0	0.7351	-0.1249	0.0058	0.4186	-0.0751	0.5858	55.1587	88.66	53.512
12	0.488	-0.114	0.3727	0.1042	-0.2048	0.4487	-0.0524	-0.5466	0.0356	-0.4144	-0.0809	-0.0103	-0.43	-0.2123	-0.0036	1.118	-0.0922	-0.1194	0.6316	-0.1002	0.7023	51.4533	96.5595	65.1523
13	0.0589	0.0288	-0.0112	0.0785	0.0731	0.0872	0.0266	0.0219	-0.525	-0.0835	0.2767	-0.2113	-0.3933	0.7306	-0.0005	0.9786	-0.1296	-0.209	0.7617	-0.1194	0.8648	62.0435	87.5674	68.0987
14	0.0995	-0.0097	-0.0683	0.1761	-0.021	0.0515	-0.3354	-0.1703	0.2728	0.2539	0.2585	-0.1463	-0.3496	-0.1039	-0.0002	0.9732	0.0233	0.0565	0.4457	-0.0233	0.5289	41.6457	86.8444	60.4489
15	0.0735	-0.2308	0.0947	0.6286	-0.3404	0.3152	-0.0142	-0.0328	-0.0088	-0.1714	0.1356	0.1481	-0.154	-0.1779	0.0001	0.4249	0.0206	0.0747	0.4151	0.0013	0.3818	33.7886	66.5401	41.3082
16	0.6211	-0.2865	-0.1339	0.4103	-0.206	0.2726	-0.1624	-0.1251	0.1987	0.048	0.1778	0.0073	0.2781	0.0841	0.0001	0.4263	-0.0234	0.0394	0.4005	-0.0291	0.3495	54.1977	63.8038	11.1906
17	0.132	-0.0917	0.0249	0.1254	0.063	0.1547	-0.2399	0.2116	0.1353	-0.2424	0.2811	-0.3131	0.2963	0.0714	0.0001	0.3374	-0.0256	0.0434	0.4939	0.0079	0.4401	62.315	75.1593	4.491
18	1.1355	-0.0557	-0.0805	0.3712	-0.4916	0.6616	0.0518	0.1395	0.1746	-0.037	0.0905	-0.0142	-0.1116	0.0177	0.0001	0.3372	-0.0515	0.0169	0.4101	-0.0045	0.4178	55.6798	80.6478	5.1604
19	0.6102	-0.3137	-0.1843	0.1771	0.0277	0.2842	-0.1119	0.045	0.086	-0.0081	0.1292	0.1572	-0.0686	0.1006	0.0002	0.3957	-0.0243	-0.0194	0.4571	-0.0539	0.482	42.3354	80.2623	2.9092
20	0.7115	0.3597	0.1451	0.4859	0.2337	0.1952	-0.1562	-0.1458	0.1957	0.0956	-0.0157	0.2909	-0.2604	0.0273	0.0002	0.3522	0.0298	-0.004	0.382	-0.0892	0.4972	41.5736	85.106	11.4521
21	0.2312	-0.0387	0.0191	0.1495	0.2436	0.3499	-0.1337	-0.0912	0.1873	-0.0487	-0.0955	0.1653	-0.0897	0.1636	0.0001	0.3625	-0.0191	-0.0535	0.4136	0.0101	0.5051	41.5324	81.67	6.3298
22	0.4129	0.1865	0.3441	2.2312	0.2875	0.248	-0.0762	-0.0578	0.1038	0.4855	0.1097	0.1317	0.3534	0.0488	-0.0004	0.3725	0.0627	0.025	0.4888	-0.0442	0.2775	51.6944	70.1499	22.2798
23	1.1976	1.2606	-0.9639	3.1513	-1.0097	2.7882	0.4346	-0.3859	0.3109	0.347	0.0651	0.2708	-0.4622	0.2189	1.8942	0.9205	0.1949	-0.4069	0.8629	-0.6078	0.9228	67.0978	90.8565	31.5868
24	0.7287	0.2166	-0.8068	0.3635	-0.0549	0.824	-0.0962	-0.4086	0.1352	0.4038	0.2738	-0.2641	0.1355	0.313	0.0366	0.3005	0.0901	-0.1435	0.5384	-0.1693	0.5165	68.874	79.8088	23.6779

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 304 THROUGH 330 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 331 THROUGH 348 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 349 THROUGH 374 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 375 THROUGH 427 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 428 THROUGH 442 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 443 THROUGH 462 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 463 THROUGH 471 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 472 THROUGH 496 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 509 THROUGH 529 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 530 THROUGH 590 )
11	X-RAY DIFFRACTION	11	CHAIN 'A' AND (RESID 591 THROUGH 631 )
12	X-RAY DIFFRACTION	12	CHAIN 'A' AND (RESID 632 THROUGH 657 )
13	X-RAY DIFFRACTION	13	CHAIN 'A' AND (RESID 658 THROUGH 678 )
14	X-RAY DIFFRACTION	14	CHAIN 'A' AND (RESID 679 THROUGH 700 )
15	X-RAY DIFFRACTION	15	CHAIN 'A' AND (RESID 701 THROUGH 752 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 304 THROUGH 348 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 349 THROUGH 374 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 375 THROUGH 412 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 413 THROUGH 442 )
20	X-RAY DIFFRACTION	20	CHAIN 'B' AND (RESID 443 THROUGH 471 )
21	X-RAY DIFFRACTION	21	CHAIN 'B' AND (RESID 472 THROUGH 497 )
22	X-RAY DIFFRACTION	22	CHAIN 'B' AND (RESID 509 THROUGH 590 )
23	X-RAY DIFFRACTION	23	CHAIN 'B' AND (RESID 591 THROUGH 631 )
24	X-RAY DIFFRACTION	24	CHAIN 'B' AND (RESID 632 THROUGH 752 )

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