[English] 日本語
Yorodumi
- PDB-7drj: Crystal structure of phosphatidylglycerol phosphate synthase in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7drj
TitleCrystal structure of phosphatidylglycerol phosphate synthase in complex with phosphatidylglycerol phosphate
ComponentsCDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
KeywordsTRANSFERASE / Product complex / Phospholipid synthase / Staphylococcus aureus / Transferase.
Function / homology
Function and homology information


CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase / CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity / phosphatidylglycerol biosynthetic process / plasma membrane
Similarity search - Function
CDP-diacylglycerol--glycerol-3-phosphate 3-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
ACETIC ACID / 1,4-BUTANEDIOL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-PO9 / CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.5 Å
AuthorsYang, B.W. / Liu, Z.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670749, 31925024 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface.
Authors: Yang, B. / Yao, H. / Li, D. / Liu, Z.
History
DepositionDec 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
B: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54330
Polymers46,3992
Non-polymers5,14428
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Target protein also exists as a dimer in detergent micelles, as revealed by size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-119 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.540, 59.376, 72.985
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number5
Space group name H-MC121
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

-
Protein , 1 types, 2 molecules AB

#1: Protein CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase / Phosphatidylglycerophosphate synthase / PGP synthase


Mass: 23199.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Staphylococcus aureus is a Gram-positive, round-shaped bacterium that is a member of the Firmicutes, and it is a usual member of the microbiota of the body, frequently found in the upper ...Details: Staphylococcus aureus is a Gram-positive, round-shaped bacterium that is a member of the Firmicutes, and it is a usual member of the microbiota of the body, frequently found in the upper respiratory tract and on the skin.
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Gene: pgsA, SA1126 / Plasmid: pET-15b
Details (production host): Ampicillin resistance; the pET-15b vector carries an N-terminal His-Tag sequence followed by a thrombin site and three cloning sites.
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: P63756, CDP-diacylglycerol-glycerol-3-phosphate 1-phosphatidyltransferase

-
Non-polymers , 6 types, 142 molecules

#2: Chemical ChemComp-PO9 / [(2R)-2-hexadecanoyloxy-3-[oxidanyl-[(2S)-2-oxidanyl-3-phosphonooxy-propoxy]phosphoryl]oxy-propyl] (Z)-octadec-9-enoate


Mass: 828.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H78O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.07 Å3/Da / Density % sol: 60 % / Description: Plate-like crystal
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 7.34
Details: 5-35% (v/v) 1,4-butanediol, 0.3M zinc acetate, 0.1M imidazole/HCl (pH 6.2-7.8)
PH range: 6.2 - 7.8

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cooling / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→33.65 Å / Num. obs: 18069 / % possible obs: 98.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 43.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.074 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.5-2.595.51.5091.117430.4850.69196.5
2.59-2.696.21.2811.417990.6710.5598.9
2.69-2.826.11.0031.918020.770.43398.7
2.82-2.9660.6642.717990.9040.28999.2
2.96-3.155.70.5363.117910.9190.2498.2
3.15-3.396.10.3485.417860.9690.1598.9
3.39-3.7360.2248.418260.9860.09699.1
3.73-4.275.70.1131518190.9950.0598.6
4.27-5.3860.08520.818380.9970.03799.5
5.38-33.655.60.05323.518660.9990.02398.2

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Blu-Ice5data collection
XDSJan 31, 2020 Built=20200417data reduction
AimlessCCP4-7.0.078data scaling
ArcimboldoCCP4-7.0.078phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.5→31.46 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 968 5.37 %Random selection
Rwork0.2123 ---
obs0.2143 18028 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 335 114 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023259
X-RAY DIFFRACTIONf_angle_d0.4674327
X-RAY DIFFRACTIONf_dihedral_angle_d20.09584
X-RAY DIFFRACTIONf_chiral_restr0.036514
X-RAY DIFFRACTIONf_plane_restr0.003502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.34531260.32042358X-RAY DIFFRACTION97
2.63-2.80.38451220.27792468X-RAY DIFFRACTION99
2.8-3.010.28831420.26032411X-RAY DIFFRACTION99
3.01-3.320.25171600.23812409X-RAY DIFFRACTION98
3.32-3.80.25831320.19932456X-RAY DIFFRACTION99
3.8-4.780.2271420.17272445X-RAY DIFFRACTION99
4.78-31.460.2021440.19172513X-RAY DIFFRACTION98

+
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