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- PDB-7ymr: Complex structure of lysoplasmalogen specific phopholipase D, F21... -

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Basic information

Entry
Database: PDB / ID: 7ymr
TitleComplex structure of lysoplasmalogen specific phopholipase D, F211L mutant with LPC
ComponentsLysoplasmalogenase
KeywordsHYDROLASE / phospholipase D / lysoplasalogen / lysoPAF / LPC
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
Chem-KIP / Lysoplasmalogenase
Similarity search - Component
Biological speciesThermocrispum sp. RD004668 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysoplasmalogenase
B: Lysoplasmalogenase
C: Lysoplasmalogenase
D: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6598
Polymers137,6724
Non-polymers1,9874
Water41423
1
A: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers34,4181
Non-polymers4971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers34,4181
Non-polymers4971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers34,4181
Non-polymers4971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysoplasmalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9152
Polymers34,4181
Non-polymers4971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)260.532, 260.532, 76.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Lysoplasmalogenase


Mass: 34418.059 Da / Num. of mol.: 4 / 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: Chemical
ChemComp-KIP / [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{5}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate


Mass: 496.638 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H51NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 4.72 Å3/Da / Density % sol: 73.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Sodium Chloride, HEPES, Ammonium Sulfate, LPC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→49.56 Å / Num. obs: 73238 / % possible obs: 99.9 % / Redundancy: 29.6 % / Biso Wilson estimate: 81.2 Å2 / CC1/2: 1 / Net I/σ(I): 25.7
Reflection shellResolution: 2.69→2.75 Å / Num. unique obs: 4425 / CC1/2: 0.568

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Processing

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

2pz0


Resolution: 2.69→48.38 Å / SU ML: 0.3814 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3518 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2435 3714 5.08 %
Rwork0.2158 69434 -
obs0.2172 73148 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.67 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9256 0 132 23 9411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00979624
X-RAY DIFFRACTIONf_angle_d1.164613116
X-RAY DIFFRACTIONf_chiral_restr0.05891456
X-RAY DIFFRACTIONf_plane_restr0.00811732
X-RAY DIFFRACTIONf_dihedral_angle_d20.98973672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.730.37961440.3532481X-RAY DIFFRACTION97.19
2.73-2.760.36121380.33652492X-RAY DIFFRACTION99.92
2.76-2.80.36821430.33992556X-RAY DIFFRACTION100
2.8-2.840.39451360.33362537X-RAY DIFFRACTION100
2.84-2.880.35791270.31022532X-RAY DIFFRACTION100
2.88-2.930.3521560.31652544X-RAY DIFFRACTION99.96
2.93-2.970.35131250.30042522X-RAY DIFFRACTION100
2.97-3.030.34181430.30922534X-RAY DIFFRACTION100
3.03-3.080.32841520.29932547X-RAY DIFFRACTION99.96
3.08-3.140.30821300.28972541X-RAY DIFFRACTION100
3.14-3.20.34081230.28112544X-RAY DIFFRACTION100
3.2-3.270.32741240.2672577X-RAY DIFFRACTION100
3.27-3.350.27651240.26782575X-RAY DIFFRACTION100
3.35-3.430.29731320.26332558X-RAY DIFFRACTION100
3.43-3.530.30731460.25712524X-RAY DIFFRACTION100
3.53-3.630.30211420.25592579X-RAY DIFFRACTION99.93
3.63-3.750.26261260.23542539X-RAY DIFFRACTION99.96
3.75-3.880.23241540.22532569X-RAY DIFFRACTION100
3.88-4.040.24641260.20562588X-RAY DIFFRACTION99.96
4.04-4.220.22441370.20152582X-RAY DIFFRACTION100
4.22-4.440.22321260.18632589X-RAY DIFFRACTION100
4.44-4.720.20131450.17472580X-RAY DIFFRACTION100
4.72-5.090.20131320.17582625X-RAY DIFFRACTION100
5.09-5.60.221440.17932595X-RAY DIFFRACTION100
5.6-6.40.22991320.19712654X-RAY DIFFRACTION100
6.4-8.060.19761600.1882645X-RAY DIFFRACTION100

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