PDB-7x0c: Crystal structure of phospholipase A1, AtDSEL

ID or keywords:

Entry

Database: PDB / ID: 7x0c

Title

Crystal structure of phospholipase A1, AtDSEL

Components

Phospholipase A1-IIgamma

Keywords

HYDROLASE / Phospholipase A1

Function / homology

Function and homology information

diacylglycerol catabolic process / negative regulation of seed germination / monoacylglycerol catabolic process / phospholipase A1 activity / monoacylglycerol lipase activity / lipid storage / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cytoplasm
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79909514333 Å

Authors

Heo, Y. / Lee, I. / Moon, S. / Lee, W.

Funding support

1items

Citation

Journal: Molecules / Year: 2022
Title: Crystal Structures of the Plant Phospholipase A1 Proteins Reveal a Unique Dimerization Domain.
Authors: Heo, Y. / Lee, I. / Moon, S. / Yun, J.H. / Kim, E.Y. / Park, S.Y. / Park, J.H. / Kim, W.T. / Lee, W.

History

Deposition	Feb 21, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x0c.cif.gz	219.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7x0c.ent.gz	139.7 KB	Display	PDB format
PDBx/mmJSON format	7x0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x0c_validation.pdf.gz	434.6 KB	Display	wwPDB validaton report
Full document	7x0c_full_validation.pdf.gz	440.6 KB	Display
Data in XML	7x0c_validation.xml.gz	32.8 KB	Display
Data in CIF	7x0c_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0c ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0c	HTTPS FTP

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Related structure data

Related structure data	7x0dC 2yijS S: Starting model for refinement C: citing same article (ref.)
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: Phospholipase A1-IIgamma

B: Phospholipase A1-IIgamma

95.8 kDa, 2 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)	73.977, 95.343, 79.278
Angle α, β, γ (deg.)	90.000, 105.144, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Phospholipase A1-IIgamma / DAD1-like seedling establishment-related lipase / AtDSEL / Phospholipase DSEL Mass: 47911.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DSEL, At4g18550, F28J12.210 / Production host: Escherichia coli (E. coli) References: UniProt: O49523, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Phospholipase A1-IIgamma / DAD1-like seedling establishment-related lipase / AtDSEL / Phospholipase DSEL

Mass: 47911.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: DSEL, At4g18550, F28J12.210 / Production host:

Escherichia coli (E. coli)
References: UniProt: O49523, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.97 Å³/Da / Density % sol: 58.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.02M calcium chloride, 0.1M sodium acetate, 30% MPD

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0082 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0082 Å / Relative weight: 1
Reflection	Resolution: 1.799→50 Å / Num. obs: 105892 / % possible obs: 99.8 % / Redundancy: 7.5 % / B_iso Wilson estimate: 22.0841058546 Å² / R_merge(I) obs: 0.086 / Net I/σ(I): 35.29
Reflection shell	Resolution: 1.8→1.86 Å / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 4586

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Processing

Software

Name: PHENIX / Version: 1.10.1_2155 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YIJ

2yij

Resolution: 1.79909514333→33.2867143454 Å / SU ML: 0.167434903764 / Cross valid method: FREE R-VALUE / σ(F): 1.35431739796 / Phase error: 19.6841137382
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.211731929786	4899	4.99464749962 %
R_work	0.178279032915	93186	-
obs	0.179912963409	98085	99.7123048146 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.9417230762 Å²

Refinement step

Cycle: LAST / Resolution: 1.79909514333→33.2867143454 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6409	0	0	423	6832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012328669973	6563
X-RAY DIFFRACTION	f_angle_d	1.12691161042	8881
X-RAY DIFFRACTION	f_chiral_restr	0.0760831334354	937
X-RAY DIFFRACTION	f_plane_restr	0.00778413893933	1159
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2582415566	3881

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 (%)
1.7991-1.8195	0.227657382375	151	0.201361485865	3009	X-RAY DIFFRACTION	98.6267166042
1.8195-1.8409	0.215272894491	167	0.190171518145	3130	X-RAY DIFFRACTION	100
1.8409-1.8634	0.240681658108	167	0.192306775035	3078	X-RAY DIFFRACTION	100
1.8634-1.887	0.246429469574	171	0.187688009829	3114	X-RAY DIFFRACTION	100
1.887-1.9118	0.221075978891	159	0.178813080001	3100	X-RAY DIFFRACTION	100
1.9118-1.938	0.199495484003	164	0.177952733986	3102	X-RAY DIFFRACTION	100
1.938-1.9657	0.24054809642	160	0.17754564755	3094	X-RAY DIFFRACTION	100
1.9657-1.995	0.222395536984	141	0.178608960118	3144	X-RAY DIFFRACTION	100
1.995-2.0262	0.215561869151	178	0.180054863732	3094	X-RAY DIFFRACTION	100
2.0262-2.0594	0.241432182807	152	0.183189729122	3120	X-RAY DIFFRACTION	100
2.0594-2.0949	0.212511469145	145	0.183303280564	3093	X-RAY DIFFRACTION	100
2.0949-2.133	0.218090952763	194	0.178715715463	3083	X-RAY DIFFRACTION	100
2.133-2.174	0.228750153827	179	0.177548906567	3134	X-RAY DIFFRACTION	100
2.174-2.2184	0.220620835796	189	0.17662366998	3061	X-RAY DIFFRACTION	99.9692402338
2.2184-2.2666	0.205116681432	153	0.177729723628	3115	X-RAY DIFFRACTION	100
2.2666-2.3193	0.223738877976	152	0.171789602439	3128	X-RAY DIFFRACTION	100
2.3193-2.3773	0.209615418273	162	0.175965166817	3107	X-RAY DIFFRACTION	99.9694189602
2.3773-2.4416	0.238820071725	170	0.178590313912	3103	X-RAY DIFFRACTION	99.9389312977
2.4416-2.5134	0.204083713643	181	0.182035288164	3102	X-RAY DIFFRACTION	99.9695493301
2.5134-2.5945	0.253452450388	163	0.178818828427	3086	X-RAY DIFFRACTION	99.9692307692
2.5945-2.6872	0.194649125562	186	0.179752388061	3103	X-RAY DIFFRACTION	99.9696048632
2.6872-2.7947	0.193533349299	164	0.174950199122	3115	X-RAY DIFFRACTION	99.9390429747
2.7947-2.9218	0.21762340366	150	0.188124013326	3137	X-RAY DIFFRACTION	100
2.9218-3.0758	0.220203616664	166	0.185981752514	3127	X-RAY DIFFRACTION	99.9393019727
3.0758-3.2683	0.226176341229	156	0.190996613246	3123	X-RAY DIFFRACTION	99.8781602193
3.2683-3.5204	0.216448041453	161	0.182772506759	3125	X-RAY DIFFRACTION	99.636143117
3.5204-3.8742	0.18170226377	158	0.185189725438	3086	X-RAY DIFFRACTION	98.6918162458
3.8742-4.4337	0.20060176688	150	0.160915349011	3108	X-RAY DIFFRACTION	98.191681736
4.4337-5.5817	0.204569946069	152	0.164173431412	3111	X-RAY DIFFRACTION	98.6993345433
5.5817-33.2867	0.189910818977	158	0.175544576077	3154	X-RAY DIFFRACTION	98.1042654028

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