PDB-6jkz: Crystal structure of VvPlpA from Vibrio vulnificus

ID or keywords:

Entry

Database: PDB / ID: 6jkz

Title

Crystal structure of VvPlpA from Vibrio vulnificus

Components

Thermolabile hemolysin

Keywords

HYDROLASE / Vibrio / phospholipase / SGNH hydrolase

Function / homology

Lipase, GDSL, active site / Lipolytic enzymes "G-D-S-L" family, serine active site. / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / lipase activity / SGNH hydrolase superfamily / lipid metabolic process / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Thermolabile hemolysin

Function and homology information

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.397 Å

Authors

Ma, Q. / Wan, Y. / Liu, C.

Funding support

China, 2items

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: Structural analysis of aVibriophospholipase reveals an unusual Ser-His-chloride catalytic triad.
Authors: Wan, Y. / Liu, C. / Ma, Q.

History

Deposition	Mar 3, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 15, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2	Aug 14, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6jkz.cif.gz	180 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6jkz_validation.pdf.gz	444.3 KB	Display	wwPDB validaton report
Full document	6jkz_full_validation.pdf.gz	445.4 KB	Display
Data in XML	6jkz_validation.xml.gz	19.5 KB	Display
Data in CIF	6jkz_validation.cif.gz	29.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jk/6jkz ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jkz	HTTPS FTP

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Related structure data

Related structure data	6jl0C 6jl1C 6jl2C C: citing same article (ref.)
Similar structure data	6jl0-d 6jl1-d 5g2t-4 3log-1 1icu-2 1ds7-d 1nec-2 6jl2-1 3veh-1 5g2u-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thermolabile hemolysin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	54.158, 54.158, 233.143
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-617- HOH

#1: Protein	Thermolabile hemolysin Mass: 48129.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN61_10355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3SYP4
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM, PPS Mass: 201.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₁NO₃S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.18 Å³/Da / Density % sol: 43.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.5 ul of protein solution (8 mg/ml in the buffer 10 mM HEPES, 150 mM NaCl, pH 7.5) and 1.5 ul of reservoir solution containing 500 mM NaCl, 10 mM MgCl2, 180 mM NDSB-201, 30% glycerine.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.397→46.902 Å / Num. obs: 79933 / % possible obs: 99.7 % / Redundancy: 18.8 % / CC_1/2: 0.998 / R_pim(I) all: 0.016 / R_rim(I) all: 0.069 / R_sym value: 0.067 / Net I/σ(I): 22
Reflection shell	Resolution: 1.397→1.421 Å / Redundancy: 12.8 % / Num. unique obs: 3826 / CC_1/2: 0.768 / R_pim(I) all: 0.255 / R_rim(I) all: 0.926 / R_sym value: 0.888 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.397→45.981 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.46

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1874	4078	5.1 %	random
R_work	0.1655	-	-	-
obs	0.1666	79896	99.68 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.397→45.981 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3194	0	27	370	3591

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3373
X-RAY DIFFRACTION	f_angle_d	0.951	4607
X-RAY DIFFRACTION	f_dihedral_angle_d	16.071	1197
X-RAY DIFFRACTION	f_chiral_restr	0.078	484
X-RAY DIFFRACTION	f_plane_restr	0.007	602

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 (%)
1.3971-1.4135	0.2735	134	0.2473	2458	X-RAY DIFFRACTION	96
1.4135-1.4308	0.2388	132	0.2367	2571	X-RAY DIFFRACTION	98
1.4308-1.4489	0.2648	145	0.2255	2544	X-RAY DIFFRACTION	100
1.4489-1.468	0.2512	138	0.2285	2626	X-RAY DIFFRACTION	100
1.468-1.4881	0.2494	141	0.2144	2534	X-RAY DIFFRACTION	100
1.4881-1.5093	0.2188	157	0.2125	2576	X-RAY DIFFRACTION	100
1.5093-1.5319	0.2186	142	0.1983	2557	X-RAY DIFFRACTION	100
1.5319-1.5558	0.2381	140	0.1935	2599	X-RAY DIFFRACTION	100
1.5558-1.5813	0.2335	148	0.1903	2564	X-RAY DIFFRACTION	100
1.5813-1.6086	0.1808	144	0.1916	2588	X-RAY DIFFRACTION	100
1.6086-1.6378	0.1968	132	0.185	2624	X-RAY DIFFRACTION	100
1.6378-1.6693	0.2205	124	0.1721	2582	X-RAY DIFFRACTION	100
1.6693-1.7034	0.2287	136	0.1801	2615	X-RAY DIFFRACTION	100
1.7034-1.7404	0.1878	162	0.1795	2600	X-RAY DIFFRACTION	100
1.7404-1.7809	0.1818	138	0.1843	2547	X-RAY DIFFRACTION	100
1.7809-1.8255	0.2069	135	0.1834	2631	X-RAY DIFFRACTION	100
1.8255-1.8748	0.209	110	0.1809	2653	X-RAY DIFFRACTION	100
1.8748-1.93	0.2285	165	0.1937	2551	X-RAY DIFFRACTION	99
1.93-1.9923	0.2181	150	0.1744	2605	X-RAY DIFFRACTION	100
1.9923-2.0635	0.2019	124	0.1676	2641	X-RAY DIFFRACTION	100
2.0635-2.1461	0.1931	132	0.1586	2621	X-RAY DIFFRACTION	100
2.1461-2.2438	0.1743	136	0.1617	2656	X-RAY DIFFRACTION	100
2.2438-2.3621	0.1928	164	0.1675	2607	X-RAY DIFFRACTION	100
2.3621-2.5101	0.1905	121	0.1599	2647	X-RAY DIFFRACTION	100
2.5101-2.7038	0.2027	135	0.1671	2688	X-RAY DIFFRACTION	100
2.7038-2.9759	0.1893	136	0.1682	2662	X-RAY DIFFRACTION	100
2.9759-3.4064	0.1608	145	0.1613	2701	X-RAY DIFFRACTION	100
3.4064-4.2912	0.1691	155	0.1365	2709	X-RAY DIFFRACTION	100
4.2912-46.0059	0.1766	157	0.164	2861	X-RAY DIFFRACTION	98

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	0.21	-0.0219	-0.0582	0.1594	0.0128	0.0702	-0.1971	-0.0421	-0.294	-0.0816	-0.1148	0.0007	0.2453	0.0458	-0.0007	0.3372	0.0936	0.0024	0.3795	-0.0422	0.3668	9.5656	0.524	91.1474
2	1.586	-0.5985	-0.0691	0.4817	0.0282	1.0035	0.0421	0.2281	-0.1414	-0.0114	-0.0288	0.0677	0.092	0.0121	-0	0.1548	0.0243	-0.0053	0.2518	-0.054	0.2029	-8.281	15.0659	82.1569
3	0.9298	-0.5606	0.2178	0.4391	0.1195	0.5853	-0.0449	-0.0487	-0.1057	0.0615	0.0464	0.0673	0.0193	0.0248	0.0005	0.1535	0.0398	0.014	0.2418	-0.0102	0.2063	-7.0563	18.8329	96.2263
4	0.3823	0.1852	0.3148	0.551	0.2426	0.4971	-0.0261	-0.0475	-0.0925	0.1352	0.1113	-0.0612	0.141	0.2189	0	0.2067	0.0846	0.0063	0.2772	-0.0186	0.2308	5.504	12.9122	98.9571
5	0.3026	0.064	0.3519	0.6864	0.4859	0.6406	-0.159	-0.0775	-0.2101	0.1357	0.0966	0.1255	0.2527	-0.249	-0.0032	0.2322	0.1108	0.0302	0.3457	0.0274	0.2106	0.6423	17.1047	112.3012
6	0.3568	0.1291	0.3479	0.0435	0.1352	0.2998	-0.0252	-0.2685	0.1373	0.0153	0.0652	0.0364	-0.0116	-0.1924	-0.0038	0.2134	0.1063	0.0077	0.4034	-0.0154	0.2395	-12.0099	27.043	114.649
7	0.1083	0.1052	0.1226	0.358	0.3955	0.5203	-0.1947	-0.3636	0.1486	0.0011	0.1751	0.0645	-0.0256	0.1344	-0.0034	0.2071	0.1035	-0.0107	0.342	-0.0356	0.2065	3.7923	27.9135	112.8655
8	1.2922	-0.2325	0.2451	0.405	0.1144	0.7329	-0.0969	-0.1093	0.1352	0.0358	0.1019	0.0389	-0.1429	-0.1175	-0.0074	0.1704	0.0764	-0.0014	0.2623	-0.0272	0.2149	-13.4435	32.1133	100.9229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 24:41)
2	X-RAY DIFFRACTION	2	(chain A and resid 42:136)
3	X-RAY DIFFRACTION	3	(chain A and resid 137:210)
4	X-RAY DIFFRACTION	4	(chain A and resid 211:242)
5	X-RAY DIFFRACTION	5	(chain A and resid 243:276)
6	X-RAY DIFFRACTION	6	(chain A and resid 277:302)
7	X-RAY DIFFRACTION	7	(chain A and resid 303:336)
8	X-RAY DIFFRACTION	8	(chain A and resid 337:422)

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