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- PDB-8ghi: Crystal structure of Staphylococcus aureus Lysophosphatidylglycer... -

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Basic information

Entry
Database: PDB / ID: 8ghi
TitleCrystal structure of Staphylococcus aureus Lysophosphatidylglycerol phospholipase D
ComponentsGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Glycerophosphodiester Phosphodiesterase (GDPD) / phospholipase D / lysophosphatidic acid / lysophosphatidylglycerol
Function / homology
Function and homology information


glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / lipid metabolic process / membrane
Similarity search - Function
Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / Glycerophosphodiester phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRock, C.O. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Lysophosphatidylglycerol (LPG) phospholipase D maintains membrane homeostasis in Staphylococcus aureus by converting LPG to lysophosphatidic acid.
Authors: Subramanian, C. / Yun, M.K. / Frank, M.M. / Rock, C.O.
History
DepositionMar 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6653
Polymers33,4761
Non-polymers1892
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.032, 108.032, 139.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

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Components

#1: Protein Glycerophosphodiester phosphodiesterase / / Glycerophosphodiester phosphodiesterase family protein / Glycerophosphoryl diester ...Glycerophosphodiester phosphodiesterase family protein / Glycerophosphoryl diester phosphodiesterase / Glycerophosphoryl diester phosphodiesterase-like protein / Putative glycerophosphoryl diester phosphodiesterase 1


Mass: 33475.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ugpQ_3, glpQ1_2, ugpQ_1, ugpQ_2, DD547_01075, EP54_07230, GO814_06870, GO942_06740, GQX37_03235, HMPREF3211_00798, NCTC13131_00521, SAGV69_01520, SAHC1335_01965, SAMEA2077334_00579, ...Gene: ugpQ_3, glpQ1_2, ugpQ_1, ugpQ_2, DD547_01075, EP54_07230, GO814_06870, GO942_06740, GQX37_03235, HMPREF3211_00798, NCTC13131_00521, SAGV69_01520, SAHC1335_01965, SAMEA2077334_00579, SAMEA2078260_00351, SAMEA2078588_00269, SAMEA2080344_00041, SAMEA2081063_00041, SAMEA2081470_00350, SAMEA70146418_01792
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6HT57, glycerophosphodiester phosphodiesterase
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Phosphate-citrate, sodium dihydrogen phosphate, dipotassium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.66 Å / Num. obs: 15817 / % possible obs: 95.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 68.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.4
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1014 / CC1/2: 0.447 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.2 Å / SU ML: 0.3351 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.9762 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 791 5 %
Rwork0.2246 15022 -
obs0.2258 15813 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 11 16 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212241
X-RAY DIFFRACTIONf_angle_d0.46833040
X-RAY DIFFRACTIONf_chiral_restr0.0405331
X-RAY DIFFRACTIONf_plane_restr0.0023397
X-RAY DIFFRACTIONf_dihedral_angle_d10.49471322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.31611340.31672551X-RAY DIFFRACTION99.63
2.55-2.750.33231350.28642541X-RAY DIFFRACTION99.26
2.75-3.020.29441320.27432524X-RAY DIFFRACTION97.29
3.02-3.460.34121330.25972528X-RAY DIFFRACTION97.26
3.46-4.360.23371240.20182352X-RAY DIFFRACTION89.45
4.36-38.20.20771330.20162526X-RAY DIFFRACTION91.56
Refinement TLS params.Method: refined / Origin x: -46.2203294685 Å / Origin y: -25.7488832149 Å / Origin z: -19.5200731997 Å
111213212223313233
T0.789752027131 Å2-0.140785370735 Å20.00884939094834 Å2-0.439166372575 Å2-0.0494517001955 Å2--0.482011679033 Å2
L3.96865392862 °2-0.446366312197 °2-0.537532339681 °2-1.66762656807 °2-0.577813575431 °2--3.22559526742 °2
S-0.278013964441 Å °0.184571872033 Å °0.0437776427239 Å °0.195076821267 Å °0.0791825562118 Å °0.14568727608 Å °-0.827289454753 Å °0.0388983231533 Å °0.191786479252 Å °
Refinement TLS groupSelection details: all

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