PDB-4nnq: Crystal structure of LnmF protein from Streptomyces amphibiosporus

ID or keywords:

Entry

Database: PDB / ID: 4nnq

Title

Crystal structure of LnmF protein from Streptomyces amphibiosporus

Components

Putative enoyl-CoA hydratase

Keywords

LYASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro /

putative enoyl-CoA hydratase

Function / homology

Function and homology information

catalytic activity
Similarity search - Function

Biological species

Streptomyces atroolivaceus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.01 Å

Authors

Michalska, K. / Bigelow, L. / Endres, M. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...

History

Deposition	Nov 18, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2014	Group: Other
Revision 1.2	Oct 29, 2014	Group: Structure summary
Revision 1.3	Nov 22, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nnq.cif.gz	270.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4nnq.ent.gz	229.9 KB	Display	PDB format
PDBx/mmJSON format	4nnq.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/nn/4nnq ftp://data.pdbj.org/pub/pdb/validation_reports/nn/4nnq	HTTPS FTP

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Related structure data

Similar structure data	4lk5-d 2b99-d 4jjt-d 3l3s-1 6y2k-d 3l3s-3 1s2g-d 6bk6-1 4f47-1 2f6q-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
Other databases	TargetTrack: MCSG-APC109429

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative enoyl-CoA hydratase

B: Putative enoyl-CoA hydratase

C: Putative enoyl-CoA hydratase

hetero molecules

86.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	104.148, 104.983, 123.247
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-301- SO4
2	1	B-301- SO4

#1: Protein	Putative enoyl-CoA hydratase / Mass: 28795.176 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces atroolivaceus (bacteria) / Gene: LnmF / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: Q8GGP6
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.95 Å³/Da / Density % sol: 36.92 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.2 M NaCl, 0.1 M CHES, 1.26 M (NH4)2SO4, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97933 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 8, 2013 / Details: mirrors

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97933 Å / Relative weight: 1

Reflection

Resolution: 2.01→30 Å / Num. all: 45198 / Num. obs: 45121 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / B_iso Wilson estimate: 32.36 Å² / R_merge(I) obs: 0.098 / Χ²: 1.348 / Net I/σ(I): 18

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.01-2.04	4.9	0.897	1.72	2244	1.128	100
2.04-2.08	5.2	0.716		2221	1.105	100
2.08-2.12	5.6	0.638		2216	1.129	100
2.12-2.17	6	0.588		2222	1.141	100
2.17-2.21	5.9	0.831		2266	1.243	100
2.21-2.26	6	0.263		2220	1.87	100
2.26-2.32	5.9	0.576		2234	1.305	100
2.32-2.38	6	0.373		2233	1.192	100
2.38-2.45	6	0.293		2271	1.18	100
2.45-2.53	6	0.221		2246	1.171	100
2.53-2.62	6	0.204		2239	1.188	100
2.62-2.73	6	0.177		2246	1.236	100
2.73-2.85	6	0.141		2259	1.247	100
2.85-3	6	0.115		2262	1.254	100
3-3.19	6	0.087		2255	1.246	100
3.19-3.44	6	0.072		2283	1.317	100
3.44-3.78	5.9	0.064		2254	1.518	99.9
3.78-4.33	5.9	0.05		2298	1.491	100
4.33-5.45	5.8	0.047		2299	1.635	99.7
5.45-30	5.5	0.054		2353	2.315	97.3

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
BUSTER-TNT	BUSTER 2.10.0	refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
SHELX		phasing
MLPHARE		phasing
DM		phasing
BUCCANEER		phasing
Coot		model building
BUSTER	2.10.0	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.01→29.06 Å / Cor.coef. F_o:F_c: 0.9563 / Cor.coef. F_o:F_c free: 0.9408 / Occupancy max: 1 / Occupancy min: 0.39 / SU R Cruickshank DPI: 0.177 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
Details: At the trimer interface there is an extra peak in the electron density map that is only partially satisfied by a sulfate ion. The remaining fragment has not been modeled.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2272	1160	2.57 %	RANDOM
R_work	0.1839	-	-	-
all	0.1849	45109	-	-
obs	0.1849	45109	99.78 %	-

Displacement parameters

B_iso max: 138.43 Å² / B_iso mean: 39.4646 Å² / B_iso min: 10.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0 Å²	0 Å²
2-	-	-0.6108 Å²	0 Å²
3-	-	-	0.2308 Å²

Refine analyze

Luzzati coordinate error obs: 0.284 Å

Refinement step

Cycle: LAST / Resolution: 2.01→29.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5163	0	20	202	5385

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	2438	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	99	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	810	HARMONIC	5
X-RAY DIFFRACTION	t_it	5299	HARMONIC	20
X-RAY DIFFRACTION	t_chiral_improper_torsion	697	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact	6392	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	5299	HARMONIC	2	0.013
X-RAY DIFFRACTION	t_angle_deg	7212	HARMONIC	2	1.08
X-RAY DIFFRACTION	t_omega_torsion				3.7
X-RAY DIFFRACTION	t_other_torsion				2.74

LS refinement shell

Resolution: 2.01→2.06 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2648	79	2.43 %
R_work	0.1936	3178	-
all	0.1953	3257	-
obs	-	3257	99.78 %

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	2.1479	-1.3385	0.2678	1.082	-2.2633	4.3639	-0.0165	0.1644	-0.1025	-0.0022	-0.1021	-0.0419	0.0236	0.188	0.1185	-0.1115	0.1091	0.1269	0.0685	0.082	0.0222	35.157	33.6899	-10.6737
2	4.637	1.7171	1.1567	3.9924	-0.368	2.5356	-0.1263	0.4107	-0.1584	-0.2795	-0.0474	-0.3186	0.4149	0.4996	0.1737	-0.0298	0.152	0.0924	-0.0688	-0.0184	0.0042	31.0364	26.5213	-5.9821
3	1.2846	0.0461	-0.2421	1.7408	-0.5981	1.3255	-0.0727	0.0554	-0.1375	-0.0451	0.0384	-0.0801	0.3211	0.2198	0.0343	0.041	0.0789	0.0241	-0.1301	0.0147	0.0742	20.9999	26.1722	4.439
4	0.2014	-1.5581	0.9367	0.9863	-0.217	0	-0.0206	0.0146	0.0028	0.068	0.0581	0.0385	-0.0833	-0.1529	-0.0375	-0.0042	0.0367	0.0097	-0.146	0.0242	0.1189	11.5381	36.6839	3.406
5	3.2986	-0.4638	0.7063	0	0.6678	1.2024	0.0389	0.2712	0.2419	-0.0258	-0.086	-0.0674	0.0078	0.3565	0.0472	-0.0587	0.023	-0.0146	-0.1564	0.0546	0.0538	24.8621	42.154	-1.1886
6	1.746	1.709	-0.3077	2.599	-0.2719	0.6043	-0.07	-0.0934	-0.1961	0.2244	0.0715	-0.3674	0.2537	0.291	-0.0015	0.0296	0.1365	-0.0149	-0.0927	0.0301	0.114	31.3019	26.5177	13.4686
7	2.1088	1.2071	0.0287	2.0985	2.7931	1.0459	0.0133	-0.0697	-0.0296	-0.0219	-0.0365	0.1256	0.001	0.0458	0.0232	0.23	0.044	0.1459	-0.2664	-0.0665	0.2533	13.8526	4.5248	1.7546
8	0	1.4879	-2.9104	0.3462	-2.1216	2.6795	-0.0365	0.0519	0.1812	0.5091	0.044	-0.0511	-0.2001	0.018	-0.0075	0.0204	-0.0176	-0.0642	-0.1262	-0.0243	0.0171	20.9204	62.7225	33.8319
9	3.0906	-1.0189	-1.1698	3.7021	-0.8785	4.7753	-0.0665	-0.34	0.2434	0.5406	0.1407	-0.5127	-0.2858	0.398	-0.0741	0.0342	-0.0274	-0.1439	-0.0993	-0.0571	0.1097	26.954	57.83	31.0276
10	1.7508	-0.6752	-0.13	1.5455	0.2077	1.4134	0.0296	-0.0522	0.0572	0.1902	0.0059	-0.3081	0.0335	0.2654	-0.0354	-0.0606	0.025	-0.0543	-0.1045	0.0154	0.068	26.2499	47.9856	20.9774
11	0	1.6856	1.224	4.9517	-1.7965	1.5296	0.0521	-0.0343	-0.2895	-0.1633	0.0126	0.0406	0.1494	-0.1241	-0.0646	-0.034	0.0283	-0.0187	-0.1194	0.0235	0.0818	15.706	47.6519	15.059
12	0.8114	-0.0417	0.1287	2.0931	-0.5402	0.1209	0.0997	-0.2209	0.0992	0.211	0.016	0.0801	-0.007	-0.0966	-0.1157	0.033	0.0342	-0.0261	-0.1133	0.0006	0.0132	10.4747	49.5188	32.6981
13	0.0936	1.494	0.5632	2.3894	0.9636	2.0996	-0.0052	-0.2989	-0.0377	0.2382	-0.0791	-0.106	0.4552	0.3166	0.0843	-0.0036	0.1514	-0.1196	-0.0291	0.0722	0.0517	29.3022	35.5313	29.2785
14	3.781	2.8995	-1.7194	1.5715	-2.6287	1.8674	-0.0631	-0.0723	0.0132	0.1114	0.2008	-0.1509	0.0145	0.472	-0.1377	-0.1423	0.0739	-0.0865	0.1011	-0.0348	0.1043	45.8727	47.5078	16.7767
15	2.6457	0.5078	-0.2024	6.2801	-0.399	0.1937	0.1058	-0.3636	-0.0697	0.4853	-0.3443	0.474	0.2314	-0.3404	0.2385	0.0481	-0.0698	0.1238	-0.1235	0.051	0.0556	-9.0419	21.5981	26.5656
16	4.109	0.1335	1.2259	3.0042	-1.3363	2.1679	0.1473	-0.2391	-0.5336	0.0175	-0.1575	0.1765	0.3868	0.0099	0.0102	0.0179	-0.0222	0.0682	-0.2294	0.1127	0.0192	-4.1843	20.5084	23.5239
17	2.2129	0.8325	0.5994	1.2108	-1.9144	2.6611	0.1205	-0.2033	-0.5144	-0.0058	-0.1823	-0.0466	0.2894	0.2613	0.0618	0.1099	0.0252	0.0213	-0.1514	0.1019	0.0819	4.9385	19.0809	28.5694
18	1.3467	0.3808	0.9758	1.0817	-0.0689	1.5651	-0.068	-0.1285	-0.0126	0.1813	-0.0308	0.0605	0.0154	0.0167	0.0988	0.0316	0.0222	0.0132	-0.1369	0.0174	0.0357	3.4277	35.3093	22.8449
19	3.1753	-0.2384	1.7324	2.2148	0.05	1.813	-0.0396	-0.1398	-0.286	-0.1108	0.0661	0.1829	0.3185	-0.1504	-0.0265	0.138	0.0424	0.0589	-0.1848	0.0316	0.0452	7.4618	16.844	11.5118
20	1.3336	1.7154	-0.2556	0.0034	-2.7993	7.5558	0.0387	-0.3603	-0.4037	0.0654	-0.0458	-0.1492	0.3054	-0.0185	0.0071	-0.0125	0.0757	-0.0622	-0.1293	0.1436	0.063	14.8775	26.594	36.0059
21	1.3882	1.3214	0.2405	1.3967	1.3229	1.2369	0.0201	-0.0158	-0.0417	0.1072	0.0829	-0.0175	0.0136	-0.0929	-0.103	0.2949	0.0343	0.0519	-0.1084	0.0597	-0.09	3.7532	38.8709	48.2782

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|10 - A\|19}	A	10 - 19
2	X-RAY DIFFRACTION	2	{A\|20 - A\|71}	A	20 - 71
3	X-RAY DIFFRACTION	3	{A\|89 - A\|174}	A	89 - 174
4	X-RAY DIFFRACTION	4	{A\|175 - A\|181}	A	175 - 181
5	X-RAY DIFFRACTION	5	{A\|182 - A\|204}	A	182 - 204
6	X-RAY DIFFRACTION	6	{A\|205 - A\|240}	A	205 - 240
7	X-RAY DIFFRACTION	7	{A\|241 - A\|254}	A	241 - 254
8	X-RAY DIFFRACTION	8	{B\|9 - B\|24}	B	9 - 24
9	X-RAY DIFFRACTION	9	{B\|25 - B\|89}	B	25 - 89
10	X-RAY DIFFRACTION	10	{B\|90 - B\|173}	B	90 - 173
11	X-RAY DIFFRACTION	11	{B\|174 - B\|187}	B	174 - 187
12	X-RAY DIFFRACTION	12	{B\|188 - B\|218}	B	188 - 218
13	X-RAY DIFFRACTION	13	{B\|219 - B\|233}	B	219 - 233
14	X-RAY DIFFRACTION	14	{B\|234 - B\|254}	B	234 - 254
15	X-RAY DIFFRACTION	15	{C\|9 - C\|44}	C	9 - 44
16	X-RAY DIFFRACTION	16	{C\|45 - C\|72}	C	45 - 72
17	X-RAY DIFFRACTION	17	{C\|87 - C\|107}	C	87 - 107
18	X-RAY DIFFRACTION	18	{C\|108 - C\|196}	C	108 - 196
19	X-RAY DIFFRACTION	19	{C\|197 - C\|221}	C	197 - 221
20	X-RAY DIFFRACTION	20	{C\|222 - C\|240}	C	222 - 240
21	X-RAY DIFFRACTION	21	{C\|241 - C\|251}	C	241 - 251

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