[English] 日本語
Yorodumi
- PDB-8ghi: Crystal structure of Staphylococcus aureus Lysophosphatidylglycer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ghi
TitleCrystal structure of Staphylococcus aureus Lysophosphatidylglycerol phospholipase D
ComponentsGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Glycerophosphodiester Phosphodiesterase (GDPD) / phospholipase D / lysophosphatidic acid / lysophosphatidylglycerol
Function / homology
Function and homology information


glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / lipid metabolic process / membrane
Similarity search - Function
Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / Glycerophosphodiester phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRock, C.O. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Lysophosphatidylglycerol (LPG) phospholipase D maintains membrane homeostasis in Staphylococcus aureus by converting LPG to lysophosphatidic acid.
Authors: Subramanian, C. / Yun, M.K. / Frank, M.M. / Rock, C.O.
History
DepositionMar 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycerophosphodiester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6653
Polymers33,4761
Non-polymers1892
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.032, 108.032, 139.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

-
Components

#1: Protein Glycerophosphodiester phosphodiesterase / Glycerophosphodiester phosphodiesterase family protein / Glycerophosphoryl diester ...Glycerophosphodiester phosphodiesterase family protein / Glycerophosphoryl diester phosphodiesterase / Glycerophosphoryl diester phosphodiesterase-like protein / Putative glycerophosphoryl diester phosphodiesterase 1


Mass: 33475.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ugpQ_3, glpQ1_2, ugpQ_1, ugpQ_2, DD547_01075, EP54_07230, GO814_06870, GO942_06740, GQX37_03235, HMPREF3211_00798, NCTC13131_00521, SAGV69_01520, SAHC1335_01965, SAMEA2077334_00579, ...Gene: ugpQ_3, glpQ1_2, ugpQ_1, ugpQ_2, DD547_01075, EP54_07230, GO814_06870, GO942_06740, GQX37_03235, HMPREF3211_00798, NCTC13131_00521, SAGV69_01520, SAHC1335_01965, SAMEA2077334_00579, SAMEA2078260_00351, SAMEA2078588_00269, SAMEA2080344_00041, SAMEA2081063_00041, SAMEA2081470_00350, SAMEA70146418_01792
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6HT57, glycerophosphodiester phosphodiesterase
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Phosphate-citrate, sodium dihydrogen phosphate, dipotassium hydrogen phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.66 Å / Num. obs: 15817 / % possible obs: 95.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 68.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.4
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1014 / CC1/2: 0.447 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.2 Å / SU ML: 0.3351 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.9762 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 791 5 %
Rwork0.2246 15022 -
obs0.2258 15813 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 11 16 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212241
X-RAY DIFFRACTIONf_angle_d0.46833040
X-RAY DIFFRACTIONf_chiral_restr0.0405331
X-RAY DIFFRACTIONf_plane_restr0.0023397
X-RAY DIFFRACTIONf_dihedral_angle_d10.49471322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.31611340.31672551X-RAY DIFFRACTION99.63
2.55-2.750.33231350.28642541X-RAY DIFFRACTION99.26
2.75-3.020.29441320.27432524X-RAY DIFFRACTION97.29
3.02-3.460.34121330.25972528X-RAY DIFFRACTION97.26
3.46-4.360.23371240.20182352X-RAY DIFFRACTION89.45
4.36-38.20.20771330.20162526X-RAY DIFFRACTION91.56
Refinement TLS params.Method: refined / Origin x: -46.2203294685 Å / Origin y: -25.7488832149 Å / Origin z: -19.5200731997 Å
111213212223313233
T0.789752027131 Å2-0.140785370735 Å20.00884939094834 Å2-0.439166372575 Å2-0.0494517001955 Å2--0.482011679033 Å2
L3.96865392862 °2-0.446366312197 °2-0.537532339681 °2-1.66762656807 °2-0.577813575431 °2--3.22559526742 °2
S-0.278013964441 Å °0.184571872033 Å °0.0437776427239 Å °0.195076821267 Å °0.0791825562118 Å °0.14568727608 Å °-0.827289454753 Å °0.0388983231533 Å °0.191786479252 Å °
Refinement TLS groupSelection details: all

+
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