PDB-4ia5: Hydratase from Lactobacillus acidophilus - SeMet derivative (apo LAH)

ID or keywords:

Entry

Database: PDB / ID: 4ia5

Title

Hydratase from Lactobacillus acidophilus - SeMet derivative (apo LAH)

Components

Myosin-crossreactive antigen

Keywords

IMMUNE SYSTEM / conjugated linoleic acid / CLA / MCRA / Rossmann fold / FAD binding / hydratase / Fatty acid

Function / homology

Function and homology information

oleate hydratase activity / FAD binding / fatty acid metabolic process
Similarity search - Function

Biological species

Lactobacillus acidophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.22 Å

Authors

Khoshnevis, S. / Neumann, P. / Ficner, R.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Crystal structure analysis of a fatty acid double-bond hydratase from Lactobacillus acidophilus
Authors: Volkov, A. / Khoshnevis, S. / Neumann, P. / Herrfurth, C. / Wohlwend, D. / Ficner, R. / Feussner, I.

History

Deposition	Dec 6, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ia5.cif.gz	492.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ia5.ent.gz	421.1 KB	Display	PDB format
PDBx/mmJSON format	4ia5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ia5_validation.pdf.gz	491.1 KB	Display	wwPDB validaton report
Full document	4ia5_full_validation.pdf.gz	521.8 KB	Display
Data in XML	4ia5_validation.xml.gz	50.1 KB	Display
Data in CIF	4ia5_validation.cif.gz	70 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ia/4ia5 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/4ia5	HTTPS FTP

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Related structure data

Related structure data	4ia6C C: citing same article (ref.)
Similar structure data	7kaz-1 7kav-2 7kaw-2 7kay-1 7kav-1 7kax-1 1wzm-d 7kay-2 5elo-2 7kax-2 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

Deposited unit

A: Myosin-crossreactive antigen

B: Myosin-crossreactive antigen

hetero molecules

139 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)	168.750, 78.970, 108.770
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	Myosin-crossreactive antigen / Hydratase Mass: 68540.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Strain: NCFM / Gene: LBA0649 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5FL96

#1: Protein

Myosin-crossreactive antigen / Hydratase

Mass: 68540.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lactobacillus acidophilus (bacteria) / Strain: NCFM / Gene: LBA0649 / Plasmid: pET24a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5FL96

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Non-polymers , 7 types, 487 molecules

#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.64 Å³/Da / Density % sol: 53.47 % Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 37% MPD, 0.1M Hepes/KOH, 10mM Phenol, 3.6mM linoleic acid, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9814 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2008

Radiation

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

Radiation wavelength

Wavelength: 0.9814 Å / Relative weight: 1

Reflection

Number: 374947 / R_merge(I) obs: 0.051 / D res high: 2.22 Å / Num. obs: 122719 / % possible obs: 88.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
6.59	44.79	5079	95.5	1	0.037
4.69	6.59	9207	97.2	1	0.039
3.83	4.69	11963	97.9	1	0.039
3.32	3.83	14166	98.1	1	0.046
2.97	3.32	16102	98.2	1	0.064
2.72	2.97	17803	98.6	1	0.096
2.51	2.72	18440	93.7	1	0.119
2.35	2.51	16998	80.5	1	0.152
2.22	2.35	12961	57.8	1	0.193

Reflection

Resolution: 2.22→50 Å / Num. obs: 122663 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 3.05 % / B_iso Wilson estimate: 39.164 Å² / R_merge(I) obs: 0.045 / Net I/σ(I): 17.76

Reflection shell

Diffraction-ID: 1

Resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.22-2.32	0.94	0.187	3.9	15159	17156	9536	0.252	55.6
2.32-2.42	0.954	0.156	4.95	18744	14455	10587	0.206	73.2
2.42-2.62	0.978	0.118	7.43	44150	22687	19941	0.149	87.9
2.62-3.4	0.996	0.069	16.47	161127	45803	44890	0.08	98
3.4-3.79	0.997	0.039	28.08	38729	10776	10559	0.046	98
3.79-4.18	0.998	0.035	31.58	25376	7113	6965	0.041	97.9
4.18-4.57	0.998	0.033	33.73	17160	4860	4763	0.039	98
4.57-14	0.998	0.033	33.89	52647	15373	14895	0.039	96.9
14-17	0.998	0.029	37.4	844	259	248	0.034	95.8
17-50	0.998	0.029	36.71	938	298	279	0.034	93.6

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHELX		phasing
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
DNA		data collection
XDS		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.22→44.791 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7713 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 29.48 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2585	6159	5.02 %	RANDOM
R_work	0.2138	-	-	-
obs	0.2161	122595	88.38 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 147.92 Å² / B_iso mean: 64.7363 Å² / B_iso min: 14.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.22→44.791 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9367	0	90	473	9930

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9692
X-RAY DIFFRACTION	f_angle_d	1.194	13130
X-RAY DIFFRACTION	f_chiral_restr	0.08	1389
X-RAY DIFFRACTION	f_plane_restr	0.006	1684
X-RAY DIFFRACTION	f_dihedral_angle_d	16.185	3603

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.22-2.2453	0.3656	114	0.3178	2089	2203	48
2.2453-2.2717	0.4089	130	0.321	2411	2541	55
2.2717-2.2994	0.4254	142	0.3047	2547	2689	59
2.2994-2.3285	0.3306	151	0.3023	2858	3009	65
2.3285-2.3591	0.303	156	0.3033	3059	3215	70
2.3591-2.3914	0.3401	171	0.3002	3238	3409	74
2.3914-2.4256	0.3601	183	0.3033	3492	3675	80
2.4256-2.4618	0.3429	190	0.2922	3587	3777	81
2.4618-2.5003	0.3358	198	0.2793	3720	3918	86
2.5003-2.5413	0.335	213	0.2814	3984	4197	89
2.5413-2.5851	0.3325	210	0.2732	3987	4197	91
2.5851-2.6321	0.3154	213	0.2673	4188	4401	94
2.6321-2.6827	0.3537	220	0.2642	4149	4369	96
2.6827-2.7374	0.2863	234	0.2722	4320	4554	98
2.7374-2.797	0.2519	227	0.254	4315	4542	99
2.797-2.862	0.3209	226	0.2549	4357	4583	99
2.862-2.9336	0.3239	226	0.2515	4319	4545	99
2.9336-3.0129	0.3326	233	0.2467	4328	4561	99
3.0129-3.1015	0.3013	229	0.2422	4270	4499	98
3.1015-3.2016	0.2698	228	0.2257	4325	4553	98
3.2016-3.316	0.2927	234	0.2173	4309	4543	98
3.316-3.4487	0.2329	229	0.2122	4360	4589	98
3.4487-3.6056	0.235	230	0.1901	4282	4512	98
3.6056-3.7956	0.2378	227	0.187	4274	4501	98
3.7956-4.0333	0.1919	226	0.1716	4314	4540	98
4.0333-4.3444	0.1981	227	0.1592	4320	4547	98
4.3444-4.7812	0.2166	228	0.1563	4280	4508	98
4.7812-5.472	0.2126	220	0.1672	4273	4493	97
5.472-6.8901	0.2012	229	0.1869	4250	4479	97
6.8901-44.7999	0.2066	215	0.1792	4231	4446	96

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	2.5147	-0.7601	-0.2425	2.1163	-0.1755	1.2999	-0.1204	0.8854	-0.5033	-0.0677	0.004	0.4961	0.2109	-0.3898	0.1002	0.3746	-0.1261	0.0329	0.5785	-0.1418	0.3333	-53.5375	5.8017	-31.0062
2	0.2947	-0.0427	-0.0475	1.1191	0.2151	0.9721	0.08	0.349	-0.3256	-0.3214	0.0981	-0.047	0.3242	-0.1305	-0.0902	0.7508	-0.3831	0.1718	0.7992	-0.8588	1.7361	-60.1296	-16.4395	-34.5728
3	1.7275	0.0012	-0.0423	0.6516	-0.1501	1.0157	-0.3308	-1.4031	0.1044	0.4118	0.234	0.287	0.0476	-0.0484	0.0805	0.5373	0.119	0.1457	0.853	-0.0767	0.2392	-53.1652	10.9805	-4.4553
4	2.2595	-0.0922	-0.2552	1.8848	-0.2069	1.4859	-0.1883	-0.4446	0.3177	0.299	0.1307	0.4075	0.0558	-0.4683	0.0627	0.3987	0.0254	0.1642	0.6641	-0.0902	0.5971	-75.7254	16.1292	-12.8656
5	1.2402	-1.6202	-0.2636	2.3048	0.3035	1.0801	-0.3257	0.1853	-0.8246	0.0938	0.0951	0.1816	0.1952	-0.0135	0.2143	0.5972	-0.1286	0.25	0.4055	-0.0282	1.2397	-60.3074	-12.5727	-20.1868
6	0.447	0.17	0.2103	1.2005	1.3989	1.6569	-0.1651	-1.0264	0.5905	0.8675	0.0142	-0.1266	-0.0169	0.1159	0.0142	0.8055	0.1491	-0.1401	0.9347	-0.5944	0.5405	-36.9853	22.0448	-1.0639
7	2.7645	0.153	-0.0409	0.8617	-0.1647	0.5163	0.0645	1.6056	2.4623	-0.03	-0.0767	-0.2899	-0.0688	0.0532	0.0146	0.4297	-0.0637	-0.0104	0.3974	0.9721	0.8814	-31.6455	28.3458	-37.6861
8	1.1862	-0.5911	-0.1058	2.1822	0.2483	0.4807	0.1416	0.342	0.414	-0.3605	-0.2891	-0.03	-0.3086	0.0313	-0.0122	0.7926	0.0027	-0.1031	0.7566	0.7617	1.9993	-28.3023	51.1962	-41.1759
9	3.7508	-0.682	0.3187	1.6293	-0.1291	0.347	-0.2386	-0.384	1.4262	0.2561	0.0893	-0.4117	-0.115	-0.004	0.1202	0.4239	-0.0203	-0.0842	0.2704	-0.0818	0.5596	-14.5628	19.2326	-18.6018
10	1.5825	-0.4878	0.1936	0.9529	-0.3631	0.4142	0.1404	2.0165	1.7458	-0.1053	-0.4396	-0.5757	-0.0689	0.0485	0.1507	0.3779	0.0185	0.0891	1.063	0.7704	0.6379	-3.639	16.5918	-40.6501
11	1.0741	-1.2675	-0.3158	1.8468	0.5338	0.1656	0.1908	0.1209	0.4356	-0.0096	0.0858	0.2066	-0.0788	-0.1041	-0.225	0.5934	-0.3139	-0.2731	0.5634	0.4664	2.0803	-18.5319	45.501	-31.1231
12	1.545	-0.763	0.2221	1.6535	-1.1272	1.0376	-0.1896	-1.2019	-0.0619	0.5166	0.131	0.0341	0.0086	0.1177	0.0602	0.5538	0.0566	0.0461	0.6602	0.0223	0.2913	-25.1037	6.2231	-7.262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	A	1 - 121
2	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	A	218 - 245
3	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	A	282 - 289
4	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	A	471 - 535
5	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 246:281 )	A	246 - 281
6	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 135:217 )	A	135 - 217
7	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )	A	290 - 311
8	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )	A	336 - 470
9	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )	A	122 - 134
10	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 312:335)	A	312 - 335
11	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 536:591 )	A	536 - 591
12	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	B	1 - 121
13	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	B	218 - 245
14	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	B	282 - 289
15	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )	B	471 - 535
16	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 246:281 )	B	246 - 281
17	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 135:217 )	B	135 - 217
18	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )	B	290 - 311
19	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )	B	336 - 470
20	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )	B	122 - 134
21	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 312:335)	B	312 - 335
22	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 536:591 )	B	536 - 591

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