PDB-8s9r: SAL2, Staphylococcus aureus lipase 2 (geh, lip2), apo form

ID or keywords:

Entry

Database: PDB / ID: 8s9r

Title

SAL2, Staphylococcus aureus lipase 2 (geh, lip2), apo form

Components

Lipase 2

Keywords

HYDROLASE / SAL2 /

Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases /

lipase / geh / SAL3 / lip2 / YP-042422.1 / WP_000943814.1 / SAOUHSC_00300 / Q2G155 / SAUSA300_0320 / NWMN_0262 / SACOL0317 / SACOL0390 / SA0309

Function / homology

Function and homology information

triacylglycerol lipase /

triglyceride lipase activity / lipid catabolic process / extracellular region
Similarity search - Function

Biological species

Staphylococcus aureus USA100-CA-126 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Fellner, M.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: SAL2, Staphylococcus aureus lipase 2 (geh, lip2), apo form
Authors: Fellner, M.

History

Deposition	Mar 30, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s9r.cif.gz	316.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8s9r.ent.gz	258.6 KB	Display	PDB format
PDBx/mmJSON format	8s9r.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/s9/8s9r ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9r	HTTPS FTP

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Related structure data

Similar structure data	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: Lipase 2

B: Lipase 2

hetero molecules

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

1

A: Lipase 2

B: Lipase 2

hetero molecules

A: Lipase 2

B: Lipase 2

hetero molecules

defined by author
Evidence: gel filtration, Shows peaks for monomer, dimer and tetramer.
179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	129.146, 129.146, 251.791
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

#1: Protein	Lipase 2 / / Glycerol ester hydrolase 2 Mass: 44467.891 Da / Num. of mol.: 2 / Fragment: N-terminal GPG from expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA100-CA-126 (bacteria) Gene: lip2, geh, SAOUHSC_00300 / Plasmid: F1002 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G155, triacylglycerol lipase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 5.9 Å³/Da / Density % sol: 79.16 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 2uL 6.1 mg/ml SAL2 (20mM Tris pH 8.0, 300mM NaCl) were mixed with 2ul of reservoir solution. Sitting drop reservoir contained 500ul of 1M ammonium phosphate and 0.1M Tris pH 8.6. Crystal was ...Details: 2uL 6.1 mg/ml SAL2 (20mM Tris pH 8.0, 300mM NaCl) were mixed with 2ul of reservoir solution. Sitting drop reservoir contained 500ul of 1M ammonium phosphate and 0.1M Tris pH 8.6. Crystal was frozen in a solution of ~25% ethylene glycol, 75% reservoir.

Crystal

Density Matthews: 5.9 Å³/Da / Density % sol: 79.16 %

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 2uL 6.1 mg/ml SAL2 (20mM Tris pH 8.0, 300mM NaCl) were mixed with 2ul of reservoir solution. Sitting drop reservoir contained 500ul of 1M ammonium phosphate and 0.1M Tris pH 8.6. Crystal was ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.6→47.58 Å / Num. obs: 66388 / % possible obs: 100 % / Redundancy: 13.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.041 / R_rim(I) all: 0.112 / Net I/σ(I): 19.1
Reflection shell	Resolution: 2.6→2.66 Å / Redundancy: 13.5 % / R_merge(I) obs: 1.649 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4385 / CC_1/2: 0.754 / R_pim(I) all: 0.666 / R_rim(I) all: 1.78 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
PHASER	2.8.3	phasing
Aimless	0.7.8	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→47.58 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.224	3232	4.88 %
R_work	0.1992	-	-
obs	0.2004	66288	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.6→47.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6039	0	19	107	6165

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6215
X-RAY DIFFRACTION	f_angle_d	0.952	8427
X-RAY DIFFRACTION	f_dihedral_angle_d	15.255	2236
X-RAY DIFFRACTION	f_chiral_restr	0.053	875
X-RAY DIFFRACTION	f_plane_restr	0.008	1097

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 (%)
2.6-2.64	0.3548	129	0.3766	2703	X-RAY DIFFRACTION	99
2.64-2.68	0.3989	138	0.3324	2711	X-RAY DIFFRACTION	100
2.68-2.72	0.3561	145	0.3078	2662	X-RAY DIFFRACTION	100
2.72-2.77	0.316	135	0.2792	2694	X-RAY DIFFRACTION	100
2.77-2.82	0.2801	140	0.2563	2712	X-RAY DIFFRACTION	100
2.82-2.87	0.289	138	0.2381	2701	X-RAY DIFFRACTION	100
2.87-2.93	0.2728	142	0.253	2703	X-RAY DIFFRACTION	100
2.93-3	0.2917	110	0.2348	2718	X-RAY DIFFRACTION	100
3-3.07	0.2537	145	0.2407	2712	X-RAY DIFFRACTION	100
3.07-3.14	0.2768	122	0.2482	2744	X-RAY DIFFRACTION	100
3.14-3.23	0.2551	149	0.2645	2693	X-RAY DIFFRACTION	100
3.23-3.32	0.2961	140	0.254	2719	X-RAY DIFFRACTION	100
3.32-3.43	0.2371	135	0.2161	2703	X-RAY DIFFRACTION	100
3.43-3.55	0.2488	138	0.2153	2736	X-RAY DIFFRACTION	100
3.55-3.69	0.2193	144	0.2074	2741	X-RAY DIFFRACTION	100
3.7-3.86	0.2151	153	0.1942	2710	X-RAY DIFFRACTION	100
3.86-4.07	0.2224	125	0.1993	2777	X-RAY DIFFRACTION	100
4.07-4.32	0.1845	152	0.1616	2741	X-RAY DIFFRACTION	100
4.32-4.65	0.1551	151	0.1544	2751	X-RAY DIFFRACTION	100
4.65-5.12	0.209	145	0.1567	2778	X-RAY DIFFRACTION	100
5.12-5.86	0.1994	135	0.1751	2817	X-RAY DIFFRACTION	100
5.86-7.38	0.1959	153	0.1781	2835	X-RAY DIFFRACTION	100
7.38-47.58	0.2069	168	0.1741	2995	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	2.5357	0.0864	-0.1428	1.5499	-0.1157	1.9671	0.0813	0.2964	-0.3408	-0.2734	-0.0879	-0.1552	0.3352	0.103	0.0091	0.4852	0.0817	0.0227	0.4438	-0.0639	0.4693	-50.7579	-44.152	-18.8913
2	4.7648	0.4806	-1.4678	2.2228	0.5888	3.0325	-0.0093	0.2142	0.1944	-0.2579	0.0289	0.1673	-0.0776	-0.3672	-0.0163	0.396	0.0293	0.0328	0.3368	0.0003	0.4149	-62.879	-38.532	-12.2285
3	0.9595	0.0622	0.0858	0.8047	-0.6285	1.8761	-0.0459	0.0333	0.1231	0.0324	0.0724	0.1551	-0.272	-0.2116	-0.0111	0.4478	0.0766	0.0495	0.4566	-0.0391	0.5343	-49.4669	-27.4898	-20.1902
4	6.4417	3.5541	-1.4525	4.7056	-0.6152	1.6614	0.2315	-0.6338	0.0217	0.2932	-0.2367	-0.415	-0.0547	0.3347	0.0071	0.4254	0.0918	-0.0212	0.5217	-0.0348	0.4146	-40.5326	-32.6613	0.303
5	6.9842	5.6307	2.9842	7.7605	0.3865	9.1083	0.2923	-0.4781	-0.8093	0.2582	-0.0911	-0.3782	0.8414	0.0037	-0.2466	0.464	0.035	0.0757	0.5304	0.0986	0.466	-49.2178	-46.7393	6.0206
6	0.363	0.8251	-1.2469	2.7403	-1.5161	6.3879	-0.2471	-0.5583	-0.3242	-0.1227	-0.1328	-0.8262	0.432	1.4123	0.3624	0.5034	0.1526	-0.0118	0.6023	0.059	0.6783	-33.6267	-42.7867	-4.9712
7	6.2599	3.8836	-2.053	3.9547	-0.5278	4.0383	0.2273	-0.5242	-1.0036	0.3369	-0.3977	-0.3994	0.6333	0.4787	0.1827	0.5871	0.1208	-0.037	0.4472	0.0733	0.6566	-43.0724	-55.7633	-4.9735
8	3.5956	0.2882	-0.26	2.7301	1.2856	6.3194	-0.0326	0.0165	0.3753	-0.2949	0.038	-0.1995	-0.6673	0.7335	-0.0148	0.4151	-0.0769	-0.0231	0.5877	0.0362	0.4404	-2.7761	-20.4401	-25.763
9	2.8091	-0.4832	-0.8279	1.8091	-1.0945	5.4824	-0.0861	0.0469	0.4136	-0.1662	-0.0344	-0.5459	-0.5628	1.3649	0.0868	0.5314	-0.1726	0.024	0.9626	-0.0424	0.5667	6.4947	-21.1386	-28.8912
10	5.2557	0.1743	-0.2814	3.617	0.9228	3.8036	-0.0581	0.9443	-0.4512	-0.55	-0.1773	-0.5758	-0.0878	1.0789	0.2664	0.621	-0.0877	0.1203	1.335	-0.1087	0.7533	15.8666	-25.7191	-41.9786
11	1.3363	-0.2971	-0.1619	1.4861	-0.3036	2.148	0.1255	-0.2562	-0.2817	-0.1386	-0.2191	-0.4329	-0.1067	0.9765	0.0791	0.4755	0.0686	-0.0276	1.0461	0.0011	0.5984	4.2639	-32.2297	-22.9747
12	4.2916	3.7702	-1.3715	4.3406	1.4341	7.2617	-0.1383	0.1697	0.4463	-0.6382	0.2672	0.1626	-0.3867	0.5525	-0.1232	0.3659	0.0025	0.0024	0.4441	0.0098	0.4633	-12.7264	-30.24	-40.9418
13	2.1978	0.9131	1.3628	2.6264	-1.028	9.3028	0.0175	0.3908	-0.3567	-0.4965	0.171	-0.167	0.9072	1.0408	-0.1489	0.5003	0.0278	0.0496	0.5219	-0.0832	0.5449	-6.9232	-36.6036	-42.1394
14	4.0759	1.4949	-0.8025	3.2837	0.707	3.7215	0.1601	-0.4706	-0.4233	0.1105	-0.2439	-0.5755	0.2855	1.1035	0.0867	0.441	0.1816	-0.0918	0.9118	0.0994	0.5718	1.1939	-37.8168	-15.0724
15	5.039	2.1182	1.4159	3.8618	0.7512	6.9504	0.1104	-1.0081	-0.9879	0.2831	0.1602	-0.6364	0.7338	0.394	-0.2775	0.5043	0.0992	-0.0386	0.8184	0.1126	0.6311	-5.5925	-44.4435	-14.9452
16	0.4899	0.4906	1.0844	1.7921	1.6881	2.7312	-0.0319	0.1562	0.105	0.1027	0.4723	-0.4537	0.2253	1.227	-0.4314	0.5454	0.1171	-0.1002	1.4894	-0.0282	0.8009	11.3458	-30.7612	-8.7875
17	1.4142	0.1037	1.454	3.923	0.347	5.2324	-0.0493	-0.8253	0.0097	0.1229	-0.0095	-0.1842	-0.4621	0.4954	0.0711	0.425	-0.0017	0.0036	0.7963	-0.0577	0.4324	-3.6212	-25.1906	-8.9313

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 109 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 110 through 151 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 152 through 243 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 244 through 315 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 316 through 337 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 338 through 363 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 364 through 385 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 88 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 131 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 132 through 151 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 152 through 181 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 182 through 218 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 219 through 243 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 244 through 285 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 286 through 315 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 316 through 337 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 338 through 385 )

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