[English] 日本語
Yorodumi
- PDB-7pow: Crystal structure of phosphatidyl serine synthase (PSS) in transi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pow
TitleCrystal structure of phosphatidyl serine synthase (PSS) in transition state.
ComponentsCDP-diacylglycerol--serine O-phosphatidyltransferaseCDP-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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein , 1 types, 2 molecules AB

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

-
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 / Chloride


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 / Serine


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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more