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- PDB-8yr6: Crystal structure of E. coli phosphatidylserine synthase complexe... -

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Basic information

Entry
Database: PDB / ID: 8yr6
TitleCrystal structure of E. coli phosphatidylserine synthase complexed with 16:0/16:0 CDP-DG
ComponentsCDP-diacylglycerol--serine O-phosphatidyltransferase
KeywordsTRANSFERASE / Complex / Phospholipid metabolism / Peripheral membrane protein / Phosphatidylserine / MEMBRANE PROTEIN
Function / homology
Function and homology information


CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity / CDP-diacylglycerol-serine O-phosphatidyltransferase / CDP-diacylglycerol-serine O-phosphatidyltransferase activity / cardiolipin biosynthetic process / phospholipid biosynthetic process / phospholipid binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CDP-alcohol phosphatidyltransferase class-II family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
: / CDP-diacylglycerol--serine O-phosphatidyltransferase PssA
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsKim, J. / Lee, E. / Cho, G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Sci Adv / Year: 2024
Title: Structural basis for membrane association and catalysis by phosphatidylserine synthase in Escherichia coli.
Authors: Lee, E. / Cho, G. / Kim, J.
History
DepositionMar 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDP-diacylglycerol--serine O-phosphatidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9823
Polymers53,9321
Non-polymers1,0502
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-5 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.497, 160.497, 160.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein CDP-diacylglycerol--serine O-phosphatidyltransferase / Phosphatidylserine synthase


Mass: 53931.781 Da / Num. of mol.: 1 / Mutation: H357A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain: str. K-12 substr. MG1655 / Cell: Bacterial / Gene: pssA, pss, b2585, JW2569 / Plasmid: modified pLATE31 / Details (production host): N-terminal His tag / Cell (production host): Bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23830, CDP-diacylglycerol-serine O-phosphatidyltransferase
#2: Chemical ChemComp-A1LZV / Cdp-DG(16:0/16:0) / 1,2-dihexadecanoyl-sn-glycero-3-cytidine-5'-diphosphate / [(2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate


Mass: 954.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H81N3O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Lithium sulfate monohydrate, 0.1 M ADA pH 6.5, 12% polyethylene glycol, 2 % (w/v) 2-propanol, 0.5 %(w/v) DDM

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→42.89 Å / Num. obs: 25695 / % possible obs: 100 % / Redundancy: 40.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.041 / Rrim(I) all: 0.26 / Χ2: 0.98 / Net I/σ(I): 11 / Num. measured all: 1041621
Reflection shellResolution: 2.44→2.54 Å / % possible obs: 100 % / Redundancy: 39.7 % / Rmerge(I) obs: 5.209 / Num. measured all: 113789 / Num. unique obs: 2868 / CC1/2: 0.483 / Rpim(I) all: 0.836 / Rrim(I) all: 5.276 / Χ2: 1.03 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MxDCdata collection
xia23.8.6data reduction
DIALS3.8data reduction
Aimless0.7.15data scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→42.89 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.324 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24698 1268 4.9 %RANDOM
Rwork0.21233 ---
obs0.21406 24360 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.996 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.44→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 69 50 3779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123806
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163698
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.8365149
X-RAY DIFFRACTIONr_angle_other_deg0.4561.7878472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.935541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89210675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6826.51775
X-RAY DIFFRACTIONr_mcbond_other1.6826.51775
X-RAY DIFFRACTIONr_mcangle_it2.79411.6862217
X-RAY DIFFRACTIONr_mcangle_other2.79411.6862218
X-RAY DIFFRACTIONr_scbond_it1.7126.7352031
X-RAY DIFFRACTIONr_scbond_other1.7096.7322028
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.98612.2932927
X-RAY DIFFRACTIONr_long_range_B_refined4.7661.684195
X-RAY DIFFRACTIONr_long_range_B_other4.76161.74191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 91 -
Rwork0.341 1745 -
obs--99.84 %

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