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- PDB-7drj: Crystal structure of phosphatidylglycerol phosphate synthase in c... -

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Basic information

Entry
Database: PDB / ID: 7drj
TitleCrystal structure of phosphatidylglycerol phosphate synthase in complex with phosphatidylglycerol phosphate
ComponentsCDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
KeywordsTRANSFERASE / Product complex / Phospholipid synthase / Staphylococcus aureus / Transferase.
Function / homology
Function and homology information


CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase / CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity / phosphatidylglycerol biosynthetic process / plasma membrane
Similarity search - Function
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature.
Similarity search - Domain/homology
ACETIC ACID / 1,4-BUTANEDIOL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-PO9 / CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.5 Å
AuthorsYang, B.W. / Liu, Z.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670749, 31925024 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface.
Authors: Yang, B. / Yao, H. / Li, D. / Liu, Z.
History
DepositionDec 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
B: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54330
Polymers46,3992
Non-polymers5,14428
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Target protein also exists as a dimer in detergent micelles, as revealed by size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-119 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.540, 59.376, 72.985
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase / Phosphatidylglycerophosphate synthase / PGP synthase


Mass: 23199.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Staphylococcus aureus is a Gram-positive, round-shaped bacterium that is a member of the Firmicutes, and it is a usual member of the microbiota of the body, frequently found in the upper ...Details: Staphylococcus aureus is a Gram-positive, round-shaped bacterium that is a member of the Firmicutes, and it is a usual member of the microbiota of the body, frequently found in the upper respiratory tract and on the skin.
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Gene: pgsA, SA1126 / Plasmid: pET-15b
Details (production host): Ampicillin resistance; the pET-15b vector carries an N-terminal His-Tag sequence followed by a thrombin site and three cloning sites.
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: P63756, CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase

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Non-polymers , 6 types, 142 molecules

#2: Chemical ChemComp-PO9 / [(2R)-2-hexadecanoyloxy-3-[oxidanyl-[(2S)-2-oxidanyl-3-phosphonooxy-propoxy]phosphoryl]oxy-propyl] (Z)-octadec-9-enoate


Mass: 828.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H78O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 60 % / Description: Plate-like crystal
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 7.34
Details: 5-35% (v/v) 1,4-butanediol, 0.3M zinc acetate, 0.1M imidazole/HCl (pH 6.2-7.8)
PH range: 6.2 - 7.8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cooling / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→33.65 Å / Num. obs: 18069 / % possible obs: 98.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 43.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.074 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.5-2.595.51.5091.117430.4850.69196.5
2.59-2.696.21.2811.417990.6710.5598.9
2.69-2.826.11.0031.918020.770.43398.7
2.82-2.9660.6642.717990.9040.28999.2
2.96-3.155.70.5363.117910.9190.2498.2
3.15-3.396.10.3485.417860.9690.1598.9
3.39-3.7360.2248.418260.9860.09699.1
3.73-4.275.70.1131518190.9950.0598.6
4.27-5.3860.08520.818380.9970.03799.5
5.38-33.655.60.05323.518660.9990.02398.2

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Blu-Ice5data collection
XDSJan 31, 2020 Built=20200417data reduction
AimlessCCP4-7.0.078data scaling
ArcimboldoCCP4-7.0.078phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.5→31.46 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 968 5.37 %Random selection
Rwork0.2123 ---
obs0.2143 18028 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 335 114 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023259
X-RAY DIFFRACTIONf_angle_d0.4674327
X-RAY DIFFRACTIONf_dihedral_angle_d20.09584
X-RAY DIFFRACTIONf_chiral_restr0.036514
X-RAY DIFFRACTIONf_plane_restr0.003502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.34531260.32042358X-RAY DIFFRACTION97
2.63-2.80.38451220.27792468X-RAY DIFFRACTION99
2.8-3.010.28831420.26032411X-RAY DIFFRACTION99
3.01-3.320.25171600.23812409X-RAY DIFFRACTION98
3.32-3.80.25831320.19932456X-RAY DIFFRACTION99
3.8-4.780.2271420.17272445X-RAY DIFFRACTION99
4.78-31.460.2021440.19172513X-RAY DIFFRACTION98

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