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

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Basic information

Entry
Database: PDB / ID: 8ghh
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: 2.1 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)34,35011
Polymers33,4761
Non-polymers87410
Water1,51384
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)107.956, 107.956, 138.381
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-571-

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


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.56 Å / Num. obs: 24165 / % possible obs: 100 % / Redundancy: 28.6 % / Biso Wilson estimate: 46.85 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.015 / Rrim(I) all: 0.081 / Net I/σ(I): 26.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1490 / Num. unique obs: 1485 / CC1/2: 0.894 / CC star: 0.966 / Rpim(I) all: 0.194 / Rrim(I) all: 0.903 / % 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: 2.1→42.56 Å / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.2141 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 1209 5 %
Rwork0.1875 22953 -
obs0.1889 24162 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2197 0 53 84 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352302
X-RAY DIFFRACTIONf_angle_d0.60443111
X-RAY DIFFRACTIONf_chiral_restr0.0452335
X-RAY DIFFRACTIONf_plane_restr0.0038400
X-RAY DIFFRACTIONf_dihedral_angle_d11.51471357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.190.30381310.25172496X-RAY DIFFRACTION99.81
2.19-2.280.27051320.23472510X-RAY DIFFRACTION100
2.28-2.410.2651330.2312513X-RAY DIFFRACTION99.96
2.41-2.560.23861320.2242519X-RAY DIFFRACTION100
2.56-2.750.2381330.21242529X-RAY DIFFRACTION100
2.75-3.030.28321340.21762543X-RAY DIFFRACTION100
3.03-3.470.23491340.1982551X-RAY DIFFRACTION100
3.47-4.370.18551370.15882577X-RAY DIFFRACTION100
4.37-42.560.18341430.16922715X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -45.7078387038 Å / Origin y: -25.7798073853 Å / Origin z: -19.3630109735 Å
111213212223313233
T0.528989310462 Å2-0.0974669100324 Å20.00943632474723 Å2-0.310928530132 Å2-0.0399088701099 Å2--0.33182336721 Å2
L3.45270942905 °2-0.541601962953 °2-0.795190275871 °2-1.48642035363 °2-0.0691876783446 °2--2.58305491936 °2
S-0.271885196002 Å °0.125195302659 Å °-0.123027193285 Å °0.12747136551 Å °-0.0110910631674 Å °0.187413980737 Å °-0.440736692246 Å °-0.0818705790274 Å °0.269248582267 Å °
Refinement TLS groupSelection details: all

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