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- PDB-7pow: Crystal structure of phosphatidyl serine synthase (PSS) in transi... -

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Basic information

Entry
Database: PDB / ID: 7pow
TitleCrystal structure of phosphatidyl serine synthase (PSS) in transition state.
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 phosphotransferase transmembrane (TM) domain / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferase, transmembrane domain / : / CDP-alcohol phosphatidyltransferase / CDP-alcohol phosphatidyltransferases signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-58A / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / SERINE / Chem-SMW / CDP-diacylglycerol--serine O-phosphatidyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsYildiz, O. / Centola, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionSep 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Nov 13, 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)51,17025
Polymers45,0412
Non-polymers6,12923
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-149 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.350, 61.220, 79.310
Angle α, β, γ (deg.)90.000, 118.723, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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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: 22520.367 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, 97 molecules

#2: Chemical ChemComp-SMW / (2S)-2-amino-3-[[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-[(2R)-2,3-bis[[(Z)-octadec-9-enoyl]oxy]propoxy]-dihydroxy-lambda^5-phosphanyl]oxy-propanoic acid / (2~{S})-2-azanyl-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-[(2~{R})-2,3-bis[[(~{Z})-octadec-9-enoyl]oxy]propoxy]-bis(oxidanyl)-$l^{5}-phosphanyl]oxy-propanoic acid


Mass: 1111.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H92N4O18P2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#7: 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.: 1 / Source method: obtained synthetically / Formula: C48H85N3O15P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.55 Å3/Da / Density % sol: 51.85 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→38.04 Å / Num. obs: 30244 / % possible obs: 98.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.05 / Rrim(I) all: 0.16 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3027 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.12 / Rrim(I) all: 0.31 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→38.04 Å / SU ML: 0.2592 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 27.1958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2757 1508 4.99 %
Rwork0.2154 28717 -
obs0.2185 30225 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.94 Å2
Refinement stepCycle: LAST / Resolution: 2.51→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 406 74 3604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753586
X-RAY DIFFRACTIONf_angle_d0.99984786
X-RAY DIFFRACTIONf_chiral_restr0.0532560
X-RAY DIFFRACTIONf_plane_restr0.0078553
X-RAY DIFFRACTIONf_dihedral_angle_d22.0518697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.590.23321310.19752553X-RAY DIFFRACTION96.34
2.59-2.680.24631360.17122583X-RAY DIFFRACTION99.31
2.68-2.790.2551400.20362631X-RAY DIFFRACTION99.93
2.79-2.910.28021370.18942594X-RAY DIFFRACTION99.85
2.91-3.070.29171400.20642667X-RAY DIFFRACTION99.86
3.07-3.260.21961370.20832594X-RAY DIFFRACTION99.93
3.26-3.510.27761390.20582609X-RAY DIFFRACTION99.96
3.51-3.860.27771360.2092651X-RAY DIFFRACTION99.93
3.87-4.420.24561380.21252613X-RAY DIFFRACTION99.96
4.42-5.570.33291360.22712628X-RAY DIFFRACTION99.96
5.57-38.040.31461380.27712594X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: -5.922 Å / Origin y: 6.707 Å / Origin z: 49.666 Å
111213212223313233
T0.146824974676 Å20.00478432391906 Å2-0.00877674151149 Å2-0.170520985387 Å2-0.0114766491246 Å2--0.178826866225 Å2
L0.589949931225 °20.122238112109 °2-0.442943875585 °2-0.655593795324 °2-0.047643295206 °2--1.1248421993 °2
S-0.0344935157629 Å °0.0505526628704 Å °-0.0237511460229 Å °0.0167073594717 Å °-0.00745497483741 Å °0.0813618688064 Å °0.0382880623526 Å °-0.110103701536 Å °0.0324580237105 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )A1 - 201
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )A301 - 306
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )A402 - 436
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )A307
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )A308 - 313
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )B-2 - 201
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )B301 - 306
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )B401 - 418
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )B307 - 310
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:201 OR RESID 301:306 OR RESID 402:436 OR RESID 307:307 OR RESID 308:313 ) ) OR ( CHAIN B AND ( RESID -2:201 OR RESID 301:306 OR RESID 401:418 OR RESID 307:310 OR RESID 419:430 ) )B419 - 430

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