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

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Basic information

Entry
Database: PDB / ID: 7drk
TitleCrystal structure of phosphatidylglycerol phosphate synthase in complex with cytidine diphosphate-diacylglycerol
ComponentsCDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
KeywordsTRANSFERASE / Substrate 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 / membrane => GO:0016020 / 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
Chem-58A / ACETIC ACID / 1,4-BUTANEDIOL / SN-GLYCEROL-3-PHOSPHATE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)51,62428
Polymers46,3992
Non-polymers5,22526
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Target protein 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 area4370 Å2
ΔGint-38 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.781, 59.432, 73.027
Angle α, β, γ (deg.)90.00, 106.66, 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 , 7 types, 130 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-58A / 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine / cytidinediphosphate-dioleoylglycerol / CDP-1,2-dioleoyl-sn-glycerol


Mass: 1006.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H85N3O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE / Glycerol 3-phosphate


Mass: 172.074 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C21H40O4
#6: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 59.88 % / Description: Plate-like crystal
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 15-26% (v/v) 1,4-butanediol, 0.2M zinc acetate, 0.1M imidazole/HCl (pH 5.0-7.5)
PH range: 5.0 - 7.5

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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: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.89→35 Å / Num. obs: 11858 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 58.93 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 5.8
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2344 / % possible all: 98.7

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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
PHASER1.17.1_3660phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DRJ

7drj


Resolution: 3→9.99 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 490 4.75 %Random selection
Rwork0.2499 ---
obs0.2523 10319 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 333 104 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043198
X-RAY DIFFRACTIONf_angle_d0.9224280
X-RAY DIFFRACTIONf_dihedral_angle_d24.449587
X-RAY DIFFRACTIONf_chiral_restr0.05510
X-RAY DIFFRACTIONf_plane_restr0.004491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.290.331280.27532451X-RAY DIFFRACTION100
3.29-3.750.31221150.24612448X-RAY DIFFRACTION100
3.75-4.640.27541320.22932408X-RAY DIFFRACTION98
4.64-9.990.30571150.26242522X-RAY DIFFRACTION99

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