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- PDB-7ym0: Lysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+ -

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Basic information

Entry
Database: PDB / ID: 7ym0
TitleLysoplasmalogen-specific phospholipase D (LyPls-PLD) with Ca2+
ComponentsLysoplasmalogenase
KeywordsHYDROLASE / phospholipase D / lisoplasmalogen / Thermocrispum / LysoPAF
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding
Similarity search - Function
Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol (PI) phosphodiesterase / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermocrispum sp. RD004668 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsYasutake, Y. / Sakasegawa, S. / Sugimori, D. / Murayama, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2022
Title: Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668.
Authors: Hamana, H. / Yasutake, Y. / Kato-Murayama, M. / Hosaka, T. / Shirouzu, M. / Sakasegawa, S.I. / Sugimori, D. / Murayama, K.
History
DepositionJul 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysoplasmalogenase
B: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3274
Polymers67,2462
Non-polymers802
Water00
1
A: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6632
Polymers33,6231
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area13020 Å2
MethodPISA
2
B: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6632
Polymers33,6231
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.952, 142.952, 126.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysoplasmalogenase


Mass: 33623.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum sp. RD004668 (bacteria) / Gene: lyspls / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4VTN7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 9.5 / Details: 0.1 M Ches pH 9.5, 50 mM NaCl, and 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.91→47.65 Å / Num. obs: 29314 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rrim(I) all: 0.111 / Net I/σ(I): 16.1
Reflection shellResolution: 2.91→3.09 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4656 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→47.29 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 1460 4.99 %
Rwork0.1769 --
obs0.1788 29256 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 2 0 4636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074756
X-RAY DIFFRACTIONf_angle_d0.846490
X-RAY DIFFRACTIONf_dihedral_angle_d21.0511768
X-RAY DIFFRACTIONf_chiral_restr0.053720
X-RAY DIFFRACTIONf_plane_restr0.006866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.0140.36731290.29612741X-RAY DIFFRACTION100
3.014-3.13460.31251530.26832728X-RAY DIFFRACTION100
3.1346-3.27730.27231440.24742715X-RAY DIFFRACTION100
3.2773-3.450.26911500.21372735X-RAY DIFFRACTION100
3.45-3.66610.22981590.19832765X-RAY DIFFRACTION100
3.6661-3.9490.20161510.17892726X-RAY DIFFRACTION100
3.949-4.34620.20671400.15892782X-RAY DIFFRACTION100
4.3462-4.97450.18631370.14152794X-RAY DIFFRACTION100
4.9745-6.2650.19181440.16852832X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.15250.89530.58563.5755-0.95312.58450.1747-0.3992-0.02970.7357-0.28750.1679-0.0319-0.03350.15390.86740.01690.0490.6294-0.0510.6678-45.897414.49350.775
22.76951.17120.29543.85230.58223.61360.1154-0.41950.11730.6102-0.17470.5429-0.26620.00920.06030.832-0.01010.12510.5430.03120.559-50.591711.87083.9297
32.1709-0.2042-1.71183.8071-1.05715.1886-0.09820.1462-0.378-0.296-0.0710.29480.7455-0.4260.15750.6975-0.0649-0.0070.45240.00930.6929-52.7292-1.4738-11.8967
44.93121.35231.45885.957-0.01477.0040.08890.37950.2835-0.14250.0343-0.0074-0.00780.051-0.16480.54420.02760.00410.47980.04460.4905-47.503314.9095-20.9295
51.8429-0.0112-0.15782.4848-1.08112.61430.0578-0.36850.02090.4668-0.239-0.2981-0.14480.47860.22080.83640.0135-0.08880.7079-0.09150.7512-26.16737.7842-11.1866
62.4575-0.63630.41065.2976-3.80246.0949-0.0183-0.0595-0.28140.1476-0.1462-0.22370.21810.6580.18910.56580.04460.00110.516-0.11920.5926-25.241337.3465-17.4745
75.35130.4263-2.02294.1270.42073.84240.3963-0.10960.92770.2936-0.04810.575-0.6922-0.1448-0.39910.88970.0270.0730.4212-0.04330.8011-37.499956.2055-15.1803
83.39030.5991-0.57275.5921-1.66114.30310.1617-0.44970.45381.0925-0.11970.6369-0.4913-0.4365-0.02710.8601-0.00650.2060.6204-0.14780.7213-45.564243.1102-5.2742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 254 )
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 333 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 133 )
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 201 )
7X-RAY DIFFRACTION7chain 'B' and (resid 202 through 275 )
8X-RAY DIFFRACTION8chain 'B' and (resid 276 through 333 )

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