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- PDB-7b1k: Crystal structure of phosphatidyl serine synthase (PSS) in the cl... -

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Basic information

Entry
Database: PDB / ID: 7b1k
TitleCrystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with bound citrate.
ComponentsCDP-diacylglycerol--serine O-phosphatidyltransferase
KeywordsLIPID BINDING PROTEIN / Membrane protein / Lipid synthase
Function / homology
Function and homology information


CDP-diacylglycerol-serine O-phosphatidyltransferase / CDP-diacylglycerol-serine O-phosphatidyltransferase activity / phospholipid biosynthetic process / plasma membrane
Similarity search - Function
CDP-diacylglycerol--serine O-phosphatidyltransferase / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature.
Similarity search - Domain/homology
Chem-58A / CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / CDP-diacylglycerol--serine O-phosphatidyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsYildiz, O. / Centola, M.
CitationJournal: Nat Commun / Year: 2021
Title: Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases
Authors: Centola, M. / Betz, H. / Yildiz, O.
History
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,46223
Polymers49,4272
Non-polymers5,03521
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-116 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.314, 70.758, 95.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 24713.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: pssA, MJ1212 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58609, CDP-diacylglycerol-serine O-phosphatidyltransferase

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Non-polymers , 8 types, 50 molecules

#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C21H40O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 300 K / Method: lipidic cubic phase
Details: Qiagens MBclass Suit and MBclass Suit II Molecular Dimension MemGold

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 2.2→57 Å / Num. obs: 31163 / % possible obs: 97.67 % / Redundancy: 7.2 % / Biso Wilson estimate: 41.58 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.08 / Rrim(I) all: 0.22 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2098 / CC1/2: 0.39 / CC star: 0.75 / Rpim(I) all: 1.07 / Rrim(I) all: 2.9 / % possible all: 96.86

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→57 Å / SU ML: 0.3983 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.9602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3071 1533 4.92 %
Rwork0.2539 29630 -
obs0.2565 31163 75.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 327 29 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223471
X-RAY DIFFRACTIONf_angle_d0.56334659
X-RAY DIFFRACTIONf_chiral_restr0.0375553
X-RAY DIFFRACTIONf_plane_restr0.003544
X-RAY DIFFRACTIONf_dihedral_angle_d22.8285607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.3823830.42091238X-RAY DIFFRACTION35.03
2.27-2.350.4252910.35281758X-RAY DIFFRACTION49.46
2.35-2.450.3941130.3711842X-RAY DIFFRACTION51.82
2.45-2.560.332860.3612225X-RAY DIFFRACTION61.59
2.56-2.690.3311140.35952546X-RAY DIFFRACTION70.41
2.69-2.860.38861330.32842812X-RAY DIFFRACTION77.95
2.86-3.080.33631450.30963348X-RAY DIFFRACTION92.85
3.08-3.390.3031700.27823496X-RAY DIFFRACTION97.6
3.39-3.880.32232280.20723441X-RAY DIFFRACTION97.27
3.88-4.890.26361880.18743445X-RAY DIFFRACTION96.47
4.89-56.860.27711820.22963479X-RAY DIFFRACTION96.95
Refinement TLS params.Method: refined / Origin x: 15.7070834764 Å / Origin y: 78.1959094882 Å / Origin z: 114.090418272 Å
111213212223313233
T0.260250032119 Å2-0.00818936966439 Å2-0.185997449491 Å2-0.242327739349 Å2-0.0251541845824 Å2--0.251539493051 Å2
L0.428521446767 °2-0.0878562205238 °2-0.0188620815215 °2-0.32338954483 °20.185099779178 °2--0.356035709001 °2
S-0.078637719497 Å °-0.05982013015 Å °-0.146073058854 Å °-0.0775132525159 Å °0.0768861339796 Å °-0.125519210662 Å °-0.0327670457907 Å °0.142359685219 Å °-0.000672538256486 Å °
Refinement TLS groupSelection details: all

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