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- PDB-7b1l: Crystal structure of phosphatidyl serine synthase (PSS) in the cl... -

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Basic information

Entry
Database: PDB / ID: 7b1l
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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / SERINE / CDP-diacylglycerol--serine O-phosphatidyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)55,56828
Polymers49,8962
Non-polymers5,67226
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-148 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.630, 79.480, 95.420
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: 24947.871 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, 127 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 39735 / % possible obs: 97.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Net I/σ(I): 936
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 3636 / CC1/2: 0.79 / CC star: 0.94 / Rpim(I) all: 0.66 / Rrim(I) all: 1.57 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→50 Å / SU ML: 0.288 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.1393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.301 3721 5 %random
Rwork0.2633 70699 --
obs0.2649 39610 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.84 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 368 101 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813491
X-RAY DIFFRACTIONf_angle_d14664
X-RAY DIFFRACTIONf_chiral_restr0.0546554
X-RAY DIFFRACTIONf_plane_restr0.0065539
X-RAY DIFFRACTIONf_dihedral_angle_d20.7769626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.4311340.42132542X-RAY DIFFRACTION92.37
1.88-1.90.39451360.39312566X-RAY DIFFRACTION94.64
1.9-1.930.37231360.37452564X-RAY DIFFRACTION93.68
1.93-1.950.40791310.34932541X-RAY DIFFRACTION94.62
1.95-1.980.39811330.33422574X-RAY DIFFRACTION94.72
1.98-2.010.42061330.2972589X-RAY DIFFRACTION96.52
2.01-2.050.29211350.28622560X-RAY DIFFRACTION94.66
2.05-2.080.28541370.27482590X-RAY DIFFRACTION95.85
2.08-2.120.32271360.25822602X-RAY DIFFRACTION94.87
2.12-2.160.26471350.25042592X-RAY DIFFRACTION96.02
2.16-2.20.33431360.24252583X-RAY DIFFRACTION94.84
2.2-2.250.32951340.24472589X-RAY DIFFRACTION96.94
2.25-2.310.25391360.24162611X-RAY DIFFRACTION95.71
2.31-2.360.27861370.22672631X-RAY DIFFRACTION96.04
2.36-2.430.22981370.22712650X-RAY DIFFRACTION98.52
2.43-2.50.28361380.23722653X-RAY DIFFRACTION97.62
2.5-2.580.33261410.22982687X-RAY DIFFRACTION97.89
2.58-2.670.27361430.22812639X-RAY DIFFRACTION98.41
2.67-2.780.26571380.23242684X-RAY DIFFRACTION98.81
2.78-2.90.26191450.22092643X-RAY DIFFRACTION98.13
2.9-3.060.28571450.23852661X-RAY DIFFRACTION97.97
3.06-3.250.25061390.24912686X-RAY DIFFRACTION97.99
3.25-3.50.27421450.23482648X-RAY DIFFRACTION99.04
3.5-3.850.24851400.24882697X-RAY DIFFRACTION98.3
3.85-4.410.32191430.26492614X-RAY DIFFRACTION97.28
4.41-5.550.30431400.292664X-RAY DIFFRACTION98.14
5.55-47.710.38321380.30582639X-RAY DIFFRACTION97.4
Refinement TLS params.Method: refined / Origin x: 15.3468722893 Å / Origin y: 86.5836083212 Å / Origin z: 18.9070062352 Å
111213212223313233
T0.151598528916 Å2-0.00396947786409 Å2-0.0154167252712 Å2-0.166631273617 Å2-0.00218869527875 Å2--0.168035885088 Å2
L0.516053413814 °2-0.0507026448513 °20.0194253802542 °2-0.907032890809 °20.000990554406104 °2--0.344998621418 °2
S0.000731608870168 Å °0.0429495828855 Å °-0.0486032818643 Å °-0.0899151249492 Å °0.0132628340203 Å °-0.0469248646585 Å °0.0257775320134 Å °0.0112995631442 Å °-0.0115510219327 Å °
Refinement TLS groupSelection details: all

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