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- PDB-7ymp: Crystal structure of lysoplasmalogen specific phospholipase D -

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Basic information

Entry
Database: PDB / ID: 7ymp
TitleCrystal structure of lysoplasmalogen specific phospholipase D
ComponentsLysoplasmalogenase
KeywordsHYDROLASE / phospholipase D / lysoplasmalogen / Thermocrispum sp. RD004668
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / Lysoplasmalogenase
Function and homology information
Biological speciesThermocrispum sp. RD004668 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Sugimori, D. / Shirouzu, M. / Hamana, H.
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 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysoplasmalogenase
B: Lysoplasmalogenase
C: Lysoplasmalogenase
D: Lysoplasmalogenase
E: Lysoplasmalogenase
F: Lysoplasmalogenase
G: Lysoplasmalogenase
H: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)275,6178
Polymers275,6178
Non-polymers00
Water5,080282
1
A: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4521
Polymers34,4521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.610, 94.940, 147.350
Angle α, β, γ (deg.)90.000, 90.243, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Lysoplasmalogenase


Mass: 34452.074 Da / Num. of mol.: 8
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG3350, Na Citrate, Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→48.43 Å / Num. obs: 98412 / % possible obs: 99.3 % / Redundancy: 5.2 % / CC1/2: 0.977 / Rrim(I) all: 0.294 / Net I/σ(I): 5.16
Reflection shellResolution: 2.57→2.73 Å / Num. unique obs: 16137 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pz0

2pz0


Resolution: 2.57→47.47 Å / SU ML: 0.4221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2754 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2717 4774 4.86 %
Rwork0.2105 93552 -
obs0.2134 98326 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.48 Å2
Refinement stepCycle: LAST / Resolution: 2.57→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18575 0 0 282 18857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008419063
X-RAY DIFFRACTIONf_angle_d1.022526014
X-RAY DIFFRACTIONf_chiral_restr0.0552889
X-RAY DIFFRACTIONf_plane_restr0.00783470
X-RAY DIFFRACTIONf_dihedral_angle_d20.90927086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.60.33351300.30763067X-RAY DIFFRACTION98.52
2.6-2.630.37661480.31653131X-RAY DIFFRACTION98.56
2.63-2.660.37431700.31363033X-RAY DIFFRACTION98.83
2.66-2.70.39651420.31243127X-RAY DIFFRACTION98.79
2.7-2.730.35661930.29523039X-RAY DIFFRACTION98.87
2.73-2.770.33721680.27823086X-RAY DIFFRACTION98.91
2.77-2.810.31041370.26053114X-RAY DIFFRACTION99
2.81-2.850.35431460.2683088X-RAY DIFFRACTION98.99
2.85-2.890.32911710.26443134X-RAY DIFFRACTION99.07
2.89-2.940.3021750.25973067X-RAY DIFFRACTION99.05
2.94-2.990.32061750.2553056X-RAY DIFFRACTION99.17
2.99-3.050.30541620.2533118X-RAY DIFFRACTION99.18
3.05-3.110.31491370.24243118X-RAY DIFFRACTION99.09
3.11-3.170.29621550.23843110X-RAY DIFFRACTION99.27
3.17-3.240.30191740.2353089X-RAY DIFFRACTION99.18
3.24-3.310.30571430.23243150X-RAY DIFFRACTION99.25
3.31-3.40.29711760.22463094X-RAY DIFFRACTION99.18
3.4-3.490.28351610.2173097X-RAY DIFFRACTION99.3
3.49-3.590.29561730.22063118X-RAY DIFFRACTION99.28
3.59-3.710.25741690.20343103X-RAY DIFFRACTION99.33
3.71-3.840.26441490.1913119X-RAY DIFFRACTION99.42
3.84-3.990.27041810.18913116X-RAY DIFFRACTION99.37
3.99-4.170.24811520.18563143X-RAY DIFFRACTION99.52
4.17-4.390.22951720.17723119X-RAY DIFFRACTION99.52
4.39-4.670.21131640.16973130X-RAY DIFFRACTION99.61
4.67-5.030.23331510.16243168X-RAY DIFFRACTION99.64
5.03-5.530.21611530.17483158X-RAY DIFFRACTION99.64
5.53-6.330.23341790.18313174X-RAY DIFFRACTION99.7
6.33-7.970.24411340.1853206X-RAY DIFFRACTION99.76
7.97-47.470.23281340.18033280X-RAY DIFFRACTION99.33

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