PDB-4ke7: Crystal structure of Monoglyceride lipase from Bacillus sp. H257 ...

ID or keywords:

Entry

Database: PDB / ID: 4ke7

Title

Crystal structure of Monoglyceride lipase from Bacillus sp. H257 in complex with an 1-myristoyl glycerol analogue

Components

Thermostable monoacylglycerol lipase

Keywords

HYDROLASE / alpha/beta hydrolase fold / monoglyceride lipase

Function / homology

Function and homology information

acylglycerol lipase / monoacylglycerol lipase activity / membrane
Similarity search - Function

Biological species

Bacillus sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.699 Å

Authors

Rengachari, S. / Aschauer, P. / Gruber, K. / Dreveny, I. / Oberer, M.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Conformational plasticity and ligand binding of bacterial monoacylglycerol lipase.
Authors: Rengachari, S. / Aschauer, P. / Schittmayer, M. / Mayer, N. / Gruber, K. / Breinbauer, R. / Birner-Gruenberger, R. / Dreveny, I. / Oberer, M.

History

Deposition	Apr 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Nov 20, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ke7.cif.gz	204.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ke7.ent.gz	171.1 KB	Display	PDB format
PDBx/mmJSON format	4ke7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ke7_validation.pdf.gz	757.9 KB	Display	wwPDB validaton report
Full document	4ke7_full_validation.pdf.gz	760.6 KB	Display
Data in XML	4ke7_validation.xml.gz	23.7 KB	Display
Data in CIF	4ke7_validation.cif.gz	34.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ke/4ke7 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4ke7	HTTPS FTP

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Related structure data

Related structure data	4ke6C 4ke8C 4ke9C 4keaC C: citing same article (ref.)
Similar structure data	3rm3-d 4kea-3 4ke6-3 4kea-2 5e1b-1 3rli-d 4kea-5 6tc4-d 1zm8-d 4dgj-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Thermostable monoacylglycerol lipase

B: Thermostable monoacylglycerol lipase

hetero molecules

60 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thermostable monoacylglycerol lipase

hetero molecules

defined by author&software
30 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thermostable monoacylglycerol lipase

hetero molecules

defined by author&software
30 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.750, 71.240, 72.900
Angle α, β, γ (deg.)	90.00, 102.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Thermostable monoacylglycerol lipase / MGLP Mass: 29560.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: H-257 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P82597, acylglycerol lipase
#2: Chemical	ChemComp-1QX / dodecyl hydrogen (S)-(3-azidopropyl)phosphonate Mass: 333.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₃₂N₃O₃P
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 408 / 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: 1.88 Å³/Da / Density % sol: 34.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD and 0.02 M alcohols (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1, 2-propanediol, 0.2 M 2-propanol, 0. ...Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD and 0.02 M alcohols (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1, 2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol), VAPOR DIFFUSION, temperature 293K

Crystal

Density Matthews: 1.88 Å³/Da / Density % sol: 34.56 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD and 0.02 M alcohols (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1, 2-propanediol, 0.2 M 2-propanol, 0. ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

EMBL/DESY, Hamburg

/ Beamline: X13 / Wavelength: 0.81 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 26, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.81 Å / Relative weight: 1

Reflection

Resolution: 1.69→71.307 Å / Num. all: 47227 / Num. obs: 47227 / % possible obs: 96.9 % / Redundancy: 3 % / R_sym value: 0.065 / Net I/σ(I): 8.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
1.69-1.78	2.8	0.215	1.8	0.215	1	87.8
1.78-1.89	3.1	0.154	4.2	0.154	1	99.8
1.89-2.02	3	0.185	2.4	0.185	1	98.8
2.02-2.19	3.1	0.078	6.5	0.078	1	99.6
2.19-2.39	2.9	0.118	2.4	0.118	1	96.2
2.39-2.68	3.1	0.048	10.9	0.048	1	99.1
2.68-3.09	3.2	0.037	16.5	0.037	1	98.7
3.09-3.79	3.1	0.042	7.1	0.042	1	97.5
3.79-5.35	3.2	0.03	16	0.03	1	97.5
5.35-23.747	3	0.071	2.5	0.071	1	95.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 1274.38 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	23.56 Å
Translation	2.5 Å	23.56 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.16	data scaling
PHASER	2.1.4	phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
DNA		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.699→23.555 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.19 / σ(F): 0.33 / Phase error: 22.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2084	2375	5.05 %
R_work	0.173	-	-
obs	0.1748	47066	97.46 %
all	-	47081	-

Solvent computation

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

Displacement parameters

B_iso mean: 13.8974 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.3496 Å²	-0 Å²	-0.6055 Å²
2-	-	-1.237 Å²	-0 Å²
3-	-	-	-0.4832 Å²

Refinement step

Cycle: LAST / Resolution: 1.699→23.555 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3768	0	58	408	4234

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3959
X-RAY DIFFRACTION	f_angle_d	1.109	5390
X-RAY DIFFRACTION	f_dihedral_angle_d	12.057	1431
X-RAY DIFFRACTION	f_chiral_restr	0.07	604
X-RAY DIFFRACTION	f_plane_restr	0.006	688

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 (%)
1.699-1.7334	0.2941	130	0.2294	2325	X-RAY DIFFRACTION	87
1.7334-1.7711	0.2275	142	0.1904	2665	X-RAY DIFFRACTION	100
1.7711-1.8123	0.2382	137	0.1755	2681	X-RAY DIFFRACTION	100
1.8123-1.8576	0.2102	138	0.1707	2663	X-RAY DIFFRACTION	100
1.8576-1.9078	0.2293	153	0.1707	2685	X-RAY DIFFRACTION	99
1.9078-1.9639	0.3024	125	0.2565	2627	X-RAY DIFFRACTION	98
1.9639-2.0273	0.2083	127	0.1672	2680	X-RAY DIFFRACTION	99
2.0273-2.0997	0.1886	132	0.1589	2687	X-RAY DIFFRACTION	99
2.0997-2.1837	0.1992	143	0.1587	2667	X-RAY DIFFRACTION	100
2.1837-2.283	0.3009	134	0.2389	2495	X-RAY DIFFRACTION	93
2.283-2.4033	0.1997	139	0.1657	2681	X-RAY DIFFRACTION	99
2.4033-2.5537	0.2189	157	0.1674	2656	X-RAY DIFFRACTION	99
2.5537-2.7506	0.2013	154	0.1635	2663	X-RAY DIFFRACTION	99
2.7506-3.0269	0.1911	132	0.1655	2648	X-RAY DIFFRACTION	98
3.0269-3.4637	0.1831	164	0.1556	2635	X-RAY DIFFRACTION	98
3.4637-4.3593	0.1525	125	0.1457	2652	X-RAY DIFFRACTION	97
4.3593-23.5574	0.1906	143	0.1638	2581	X-RAY DIFFRACTION	93

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	2.2699	1.2861	-0.7869	1.9442	-0.5707	0.9228	-0.1006	0.0555	-0.1902	-0.1754	0.0183	-0.2346	0.1332	0.0815	0.0777	0.0728	0.0043	0.01	0.0615	0.0049	0.0661	7.3223	-5.231	25.8152
2	1.0415	-0.3518	-0.5045	1.5961	0.234	1.5838	0.0354	0.2062	0.0104	-0.174	-0.009	0.1207	0.0413	-0.1222	-0.0206	0.0605	-0.0021	-0.0151	0.0701	0.0049	0.0452	-4.0375	0.4062	24.7946
3	1.7487	0.8817	-2.1278	0.693	-0.5553	3.5024	0.1258	0.0129	0.1433	-0.0045	0.0666	-0.007	-0.4257	0.183	-0.119	0.1516	-0.0343	0.0007	0.1116	0.0025	0.1251	15.4699	8.1375	32.543
4	5.368	-0.5315	-1.3115	1.3531	-0.0178	1.3182	0.1004	0.2161	0.4926	-0.2217	-0.0288	-0.0599	-0.1898	0.0257	-0.0221	0.1199	-0.015	0.0065	0.0779	0.032	0.0865	3.6085	12.8567	22.1151
5	3.1354	-0.2136	0.596	1.2881	-0.3016	0.9888	0.0213	-0.1804	0.1002	0.1424	-0.041	0.0816	-0.0458	-0.0914	0.024	0.0746	-0.0032	0.0076	0.0499	-0.0058	0.0308	-5.8109	6.7135	37.4684
6	9.4584	3.8249	4.131	2.4616	1.0374	2.5137	0.2304	-0.5074	0.0227	0.2129	-0.2546	0.1759	0.0256	-0.2043	0.0289	0.1413	-0.0211	0.022	0.0748	0.012	0.0685	-5.5485	-6.2125	41.43
7	4.9357	3.7923	-4.6452	4.9775	-2.8913	7.0141	-0.1769	0.2441	-0.1972	-0.1193	0.1317	-0.1839	0.1103	0.1104	-0.0646	0.1061	0.0288	0.0483	0.1052	-0.0298	0.1792	30.27	-3.7421	56.022
8	2.2807	1.1031	-0.396	2.1923	-0.4305	1.0535	-0.043	0.1903	-0.1427	-0.0958	0.0019	-0.1818	0.1144	0.043	0.0436	0.0618	0.008	0.0064	0.0631	-0.004	0.0436	19.7787	-4.8482	62.3438
9	2.5701	2.7641	0.0642	8.9545	-0.6169	2.3658	-0.0681	0.2118	-0.0049	-0.3332	-0.0132	0.2779	0.0455	-0.1383	0.0251	0.0774	0.0101	-0.0181	0.1167	-0.0156	0.0391	11.3929	-4.4922	54.7917
10	0.8838	-0.7575	-0.6898	1.0996	-0.2829	1.6013	0.0601	0.1744	0.1924	-0.0333	-0.0063	-0.0021	-0.0809	-0.064	-0.0264	0.0598	0.0033	-0.016	0.0655	0.0177	0.0633	12.441	5.6675	63.2271
11	1.8962	-0.1584	-3.4295	-0.0015	0.2778	6.1604	0.2098	-0.1129	-0.0479	0.2034	0.0684	-0.3278	-0.0155	0.4706	-0.2243	0.1447	-0.0396	-0.0617	0.1952	-0.0138	0.1648	29.2605	3.43	72.9829
12	6.2105	0.3782	-1.9723	1.6703	-0.4448	1.6057	0.1177	0.355	0.5069	-0.1642	0.0206	-0.001	-0.1974	-0.1068	-0.1093	0.1394	0.0123	0.0036	0.0693	0.0314	0.0842	14.4652	12.8493	58.8413
13	2.4165	-0.3985	0.5605	1.0199	-0.4895	1.4604	0.0345	-0.1101	0.0505	0.1493	-0.0002	0.1269	-0.0881	-0.0527	-0.0359	0.0861	-0.0043	0.0093	0.0352	-0.0103	0.0542	9.6367	6.4441	74.8941
14	2.1152	3.0143	5.2514	2.7767	0.6308	4.2695	0.0034	-0.596	0.1833	0.3006	-0.1059	0.3201	0.1435	-0.3706	0.0019	0.1062	-0.0099	0.0352	0.1056	-0.0242	0.091	8.7607	-6.4541	76.6927

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:69)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 70:131)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 132:160)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 161:179)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 180:231)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 232:250)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 2:13)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 14:69)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 70:89)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 90:143)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 144:160)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 161:183)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 184:231)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 232:250)

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