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- PDB-8yr5: Crystal structure of E. coli phosphatidylserine synthase in apo state -

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Basic information

Entry
Database: PDB / ID: 8yr5
TitleCrystal structure of E. coli phosphatidylserine synthase in apo state
ComponentsCDP-diacylglycerol--serine O-phosphatidyltransferase
KeywordsTRANSFERASE / Apo / 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
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: CDP-diacylglycerol--serine O-phosphatidyltransferase
B: CDP-diacylglycerol--serine O-phosphatidyltransferase
C: CDP-diacylglycerol--serine O-phosphatidyltransferase
D: CDP-diacylglycerol--serine O-phosphatidyltransferase
E: CDP-diacylglycerol--serine O-phosphatidyltransferase
F: CDP-diacylglycerol--serine O-phosphatidyltransferase
G: CDP-diacylglycerol--serine O-phosphatidyltransferase
H: CDP-diacylglycerol--serine O-phosphatidyltransferase
I: CDP-diacylglycerol--serine O-phosphatidyltransferase
J: CDP-diacylglycerol--serine O-phosphatidyltransferase
K: CDP-diacylglycerol--serine O-phosphatidyltransferase
L: CDP-diacylglycerol--serine O-phosphatidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)650,29236
Polymers647,98612
Non-polymers2,30624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.040, 94.100, 194.750
Angle α, β, γ (deg.)88.24, 87.70, 60.07
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 53998.848 Da / Num. of mol.: 12
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.09 M Sodium citrate tribasic dihydrate pH 5.9, 0.09 M Lithium sulfate monohydrate, 0.1 M Sodium malonate pH 7.0, 12.6 % (w/v) polyethylene glycol 4000

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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: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→48.64 Å / Num. obs: 135369 / % possible obs: 98.2 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.088 / Rrim(I) all: 0.207 / Χ2: 1.09 / Net I/σ(I): 8.1 / Num. measured all: 722456
Reflection shellResolution: 2.83→2.88 Å / % possible obs: 98 % / Redundancy: 5.3 % / Rmerge(I) obs: 1.86 / Num. measured all: 35555 / Num. unique obs: 6672 / CC1/2: 0.36 / Rpim(I) all: 0.882 / Rrim(I) all: 2.063 / Χ2: 0.99 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
MxDCdata collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0425refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→48.64 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.896 / SU B: 30.252 / SU ML: 0.532 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28478 6358 4.7 %RANDOM
Rwork0.2419 ---
obs0.24394 129010 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å23.5 Å2-2.14 Å2
2--1.94 Å2-1.01 Å2
3---2.8 Å2
Refinement stepCycle: 1 / Resolution: 2.83→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43775 0 120 0 43895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01244800
X-RAY DIFFRACTIONr_bond_other_d0.0010.01643374
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.83960662
X-RAY DIFFRACTIONr_angle_other_deg0.4771.79599253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84455261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.0635471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.865108115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.26633
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0253722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211054
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_it5.8646.90621107
X-RAY DIFFRACTIONr_mcbond_other5.8646.90621107
X-RAY DIFFRACTIONr_mcangle_it9.24312.40926347
X-RAY DIFFRACTIONr_mcangle_other9.24312.40926348
X-RAY DIFFRACTIONr_scbond_it5.6827.32423693
X-RAY DIFFRACTIONr_scbond_other5.6587.32223598
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.25713.26734172
X-RAY DIFFRACTIONr_long_range_B_refined12.76369.748773
X-RAY DIFFRACTIONr_long_range_B_other12.76369.748774
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 450 -
Rwork0.378 9485 -
obs--97.91 %

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