PDB-6i8w: Crystal structure of a membrane phospholipase A, a novel bacteria...

ID or keywords:

Entry

Database: PDB / ID: 6i8w

Title

Crystal structure of a membrane phospholipase A, a novel bacterial virulence factor

Components

Alpha/beta fold hydrolase

Keywords

HYDROLASE / Lipase / Membrane Protein

Function / homology

Function and homology information

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

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Granzin, J. / Batra-Safferling, R.

Citation

Journal: Elife / Year: 2022
Title: Structural, mechanistic, and physiological insights into phospholipase A-mediated membrane phospholipid degradation in Pseudomonas aeruginosa.
Authors: Bleffert, F. / Granzin, J. / Caliskan, M. / Schott-Verdugo, S.N. / Siebers, M. / Thiele, B. / Rahme, L. / Felgner, S. / Dormann, P. / Gohlke, H. / Batra-Safferling, R. / Jaeger, K.E. / Kovacic, F.

History

Deposition	Nov 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2020	Group: Database references / Category: citation / Item: _citation.title
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	May 18, 2022	Group: Database references / Structure summary Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Apr 26, 2023	Group: Database references / Structure summary / Category: citation / citation_author / entity_name_com Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _entity_name_com.name
Revision 1.5	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6i8w.cif.gz	265.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6i8w_validation.pdf.gz	921.5 KB	Display	wwPDB validaton report
Full document	6i8w_full_validation.pdf.gz	927.9 KB	Display
Data in XML	6i8w_validation.xml.gz	26.9 KB	Display
Data in CIF	6i8w_validation.cif.gz	37.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i8/6i8w ftp://data.pdbj.org/pub/pdb/validation_reports/i8/6i8w	HTTPS FTP

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Related structure data

Related structure data	2vf2S S: Starting model for refinement
Similar structure data	1438 7nmj-3 7nmj-2 7nmj-1 2ghr-d 5mhb-d 1b4e-d 7nmj-4 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
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #165 - Sep 2013 Designed Protein Cages similarity (3) #220 - Apr 2018 Dehalogenases similarity (3) #143 - Nov 2011 Toll-like Receptors similarity (1) #20 - Aug 2001 Poliovirus and Rhinovirus similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#263 - Nov 2021
Acetohydroxyacid Synthase
similarity (1)
#165 - Sep 2013
Designed Protein Cages
similarity (3)
#220 - Apr 2018
Dehalogenases
similarity (3)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#20 - Aug 2001
Poliovirus and Rhinovirus
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#216 - Dec 2017
Biodegradable Plastic
similarity (1)
#70 - Oct 2005
Designer Proteins
similarity (1)

Deposited unit

A: Alpha/beta fold hydrolase

B: Alpha/beta fold hydrolase

hetero molecules

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

1

A: Alpha/beta fold hydrolase

hetero molecules

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

2

B: Alpha/beta fold hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	133.871, 133.871, 212.358
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

Alpha/beta fold hydrolase / Esterase / Lipase / Lipase 3 / Putative lipase / PlaF

Mass: 35792.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FME:N-Formylmethionine, C-terminal His-Tag / Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria)
Gene: lip3, AOY09_04297, C8257_11100, DN070_25360, NCTC13719_02038, PAMH19_2121
Production host:

Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9KJG6, triacylglycerol lipase

#3: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

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Non-polymers , 5 types, 243 molecules

#2: Chemical	ChemComp-MYR / MYRISTIC ACID Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₈O₂
#4: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#5: Chemical	ChemComp-CO2 / CARBON DIOXIDE Mass: 44.010 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO₂
#6: Chemical	ChemComp-11A / UNDECANOIC ACID Mass: 186.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₂O₂ / Comment: antifungal*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 58 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Trisodium citrate, 10% (w/v) PEG 4000, 10% (w/v) Isopropanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9686 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014
Radiation	Monochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 2→47.33 Å / Num. obs: 65113 / % possible obs: 100 % / Redundancy: 10.3 % / B_iso Wilson estimate: 38.3 Å² / CC_1/2: 1 / R_merge(I) obs: 0.053 / R_pim(I) all: 0.017 / R_rim(I) all: 0.056 / Net I/σ(I): 24.6
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4527 / CC_1/2: 0.789 / R_pim(I) all: 0.307 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
XDS		data reduction
Aimless		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VF2

2vf2

Resolution: 2→47.33 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.61

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1857	3298	5.07 %	Random selection
R_work	0.163	-	-	-
obs	0.1642	65084	99.96 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å

Refinement step

Cycle: LAST / Resolution: 2→47.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4763	0	96	233	5092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5067
X-RAY DIFFRACTION	f_angle_d	1.069	6892
X-RAY DIFFRACTION	f_dihedral_angle_d	14.404	1914
X-RAY DIFFRACTION	f_chiral_restr	0.047	786
X-RAY DIFFRACTION	f_plane_restr	0.006	904

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 (%)
2-2.0286	0.2672	140	0.241	2551	X-RAY DIFFRACTION	100
2.0286-2.0589	0.2571	134	0.2216	2559	X-RAY DIFFRACTION	100
2.0589-2.091	0.2914	142	0.2142	2542	X-RAY DIFFRACTION	100
2.091-2.1253	0.2411	144	0.2009	2527	X-RAY DIFFRACTION	100
2.1253-2.162	0.2512	132	0.1967	2535	X-RAY DIFFRACTION	100
2.162-2.2013	0.2074	140	0.1815	2529	X-RAY DIFFRACTION	100
2.2013-2.2436	0.2261	125	0.1687	2542	X-RAY DIFFRACTION	100
2.2436-2.2894	0.1783	155	0.161	2532	X-RAY DIFFRACTION	100
2.2894-2.3392	0.2015	126	0.1591	2567	X-RAY DIFFRACTION	100
2.3392-2.3936	0.1957	133	0.1606	2560	X-RAY DIFFRACTION	100
2.3936-2.4535	0.1998	147	0.1636	2536	X-RAY DIFFRACTION	100
2.4535-2.5198	0.1916	148	0.1588	2547	X-RAY DIFFRACTION	100
2.5198-2.5939	0.1931	132	0.1643	2571	X-RAY DIFFRACTION	100
2.5939-2.6776	0.1879	145	0.165	2554	X-RAY DIFFRACTION	100
2.6776-2.7733	0.197	126	0.1734	2554	X-RAY DIFFRACTION	100
2.7733-2.8844	0.2119	137	0.1728	2578	X-RAY DIFFRACTION	100
2.8844-3.0156	0.2104	124	0.1777	2578	X-RAY DIFFRACTION	100
3.0156-3.1746	0.2145	131	0.1829	2588	X-RAY DIFFRACTION	100
3.1746-3.3734	0.1752	146	0.1687	2584	X-RAY DIFFRACTION	100
3.3734-3.6338	0.1508	147	0.1597	2589	X-RAY DIFFRACTION	100
3.6338-3.9993	0.1695	132	0.1491	2600	X-RAY DIFFRACTION	100
3.9993-4.5776	0.1468	129	0.1327	2634	X-RAY DIFFRACTION	100
4.5776-5.7657	0.1858	143	0.1439	2652	X-RAY DIFFRACTION	100
5.7657-47.3438	0.1784	140	0.1738	2777	X-RAY DIFFRACTION	99

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	4.3437	2.1782	-0.4565	1.8875	-1.3233	7.5132	0.3162	-0.6284	1.8362	0.2078	0.1453	-0.4678	-0.9295	2.0465	-0.4707	0.9217	-0.3696	-0.0049	0.9527	-0.1194	1.2703	104.4359	38.4985	11.9893
2	1.6301	-0.5828	-0.1443	1.872	-1.2341	1.9623	-0.0391	0.3787	0.2315	-0.1372	-0.2545	-0.4322	-0.1747	0.3248	0.2613	0.3944	-0.0108	-0.0093	0.3131	0.1649	0.3537	75.3587	22.8505	-1.1034
3	2.1159	1.0394	-0.7326	2.6173	-0.5894	2.8367	-0.0447	0.3563	0.4554	-0.0341	0.0073	0.0929	-0.2502	-0.1082	0.0407	0.3416	0.0114	-0.0063	0.2437	0.1213	0.321	63.0905	27.0606	-0.9302
4	3.3722	-0.2335	0.5134	5.8023	1.994	3.6835	0.046	0.0231	0.6246	0.2288	-0.1418	0.87	-0.1709	-0.4392	0.0438	0.2896	0.0002	0.066	0.2329	0.0883	0.445	51.3149	28.9932	4.9707
5	3.0668	-1.116	0.64	3.2946	0.0837	2.0403	-0.0167	-0.2572	0.4913	0.8152	-0.0995	-0.177	-0.7771	0.2307	0.0951	0.862	-0.1788	0.0203	0.365	-0.0164	0.469	66.5276	35.6845	19.4903
6	3.0371	-3.8164	2.3359	5.829	-1.9962	4.3952	0.0005	-0.3598	0.9972	0.1746	-0.1722	-0.6093	-0.7122	0.3535	0.1967	0.6324	-0.1167	-0.0146	0.3389	0.0978	0.5516	71.7484	38.5745	9.9212
7	2.3011	1.506	-0.5168	3.3587	-0.5145	1.2997	0.1948	0.0895	0.6983	0.5032	-0.1022	0.6973	-0.3784	-0.234	-0.0927	0.4041	0.031	0.1247	0.2337	0.018	0.4434	51.1457	26.7629	10.7793
8	2.4956	-1.8894	3.4552	2.257	-0.9575	8.5445	0.2302	0.1329	-0.5182	0.1399	-0.1609	0.374	0.6341	-0.325	-0.112	0.404	-0.0293	0.06	0.2947	-0.0246	0.3579	55.5978	11.7793	6.6377
9	4.3209	5.2474	-1.1194	6.0737	-1.3276	0.1672	0.4361	0.1774	-0.5389	0.5568	-0.1441	-1.5693	-0.2204	0.2786	-0.139	0.6294	-0.1557	0.0445	0.5195	0.1393	0.8006	97.9057	30.3156	5.8969
10	3.178	0.7353	1.4265	2.0848	0.9889	3.7494	-0.1129	0.2281	0.043	0.0094	0.1218	-0.254	-0.0898	0.3953	-0.0103	0.3201	-0.0398	-0.1151	0.2711	0.0808	0.2923	93.294	-2.0457	21.3392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 149 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 171 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 172 through 207 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 208 through 234 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 235 through 292 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 293 through 310 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 37 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 310 )

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