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- PDB-7ymq: Crystal structure of lysoplasmalogen specific phopholipase D, F21... -

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Basic information

Entry
Database: PDB / ID: 7ymq
TitleCrystal structure of lysoplasmalogen specific phopholipase D, F211L mutant
ComponentsLysoplasmalogenase
KeywordsHYDROLASE / phospholipase D / lysoplasmalogen / F211L murant
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: 2.29 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)275,3448
Polymers275,3448
Non-polymers00
Water11,187621
1
A: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.570, 93.750, 147.810
Angle α, β, γ (deg.)90.000, 90.360, 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: 34418.059 Da / Num. of mol.: 8 / Mutation: F211L
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.: 621 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 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: 2.29→47.94 Å / Num. obs: 129674 / % possible obs: 94.4 % / Redundancy: 3.5 % / CC1/2: 0.987 / Net I/σ(I): 5.7
Reflection shellResolution: 2.29→2.43 Å / Num. unique obs: 21072 / CC1/2: 0.549

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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: 2.29→46.88 Å / SU ML: 0.3378 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.55 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2373 6577 5.08 %
Rwork0.1849 122898 -
obs0.1875 129475 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.44 Å2
Refinement stepCycle: LAST / Resolution: 2.29→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18551 0 0 621 19172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008219031
X-RAY DIFFRACTIONf_angle_d0.945925974
X-RAY DIFFRACTIONf_chiral_restr0.0532897
X-RAY DIFFRACTIONf_plane_restr0.00723462
X-RAY DIFFRACTIONf_dihedral_angle_d3.148511520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.32362180.29384029X-RAY DIFFRACTION93.46
2.32-2.340.33982350.28534051X-RAY DIFFRACTION93.77
2.34-2.370.34952230.28084067X-RAY DIFFRACTION94.26
2.37-2.40.30992030.25734087X-RAY DIFFRACTION94.51
2.4-2.430.31411880.2554075X-RAY DIFFRACTION93.77
2.43-2.470.31622320.24944076X-RAY DIFFRACTION94.1
2.47-2.50.31091890.25154067X-RAY DIFFRACTION93.68
2.5-2.540.30972140.25144036X-RAY DIFFRACTION93.18
2.54-2.580.32062420.24533835X-RAY DIFFRACTION90.56
2.58-2.620.31522030.23923931X-RAY DIFFRACTION90.52
2.62-2.670.32182010.2364119X-RAY DIFFRACTION94.45
2.67-2.720.27062280.22864145X-RAY DIFFRACTION96.07
2.72-2.770.28882120.2284156X-RAY DIFFRACTION96.06
2.77-2.820.29382010.24044172X-RAY DIFFRACTION95.73
2.82-2.890.31112290.24624141X-RAY DIFFRACTION96.02
2.89-2.950.32852310.22964159X-RAY DIFFRACTION95.83
2.95-3.030.26172380.2214177X-RAY DIFFRACTION96.04
3.03-3.110.28891990.2154149X-RAY DIFFRACTION95.5
3.11-3.20.27242160.2164131X-RAY DIFFRACTION95.64
3.2-3.30.26452360.21224143X-RAY DIFFRACTION95.34
3.3-3.420.28212540.21064058X-RAY DIFFRACTION95.15
3.42-3.560.26272410.19484162X-RAY DIFFRACTION95.3
3.56-3.720.19961880.17714191X-RAY DIFFRACTION95.55
3.72-3.920.21852180.16584139X-RAY DIFFRACTION95.05
3.92-4.160.21872220.15824083X-RAY DIFFRACTION94
4.16-4.480.2062030.14614107X-RAY DIFFRACTION93.65
4.48-4.930.17071970.13123957X-RAY DIFFRACTION90.66
4.93-5.640.18822420.13914177X-RAY DIFFRACTION95.42
5.64-7.110.19292450.15174186X-RAY DIFFRACTION95.56
7.11-46.880.15662290.13574092X-RAY DIFFRACTION91.01

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