[English] 日本語
Yorodumi
- PDB-7ymq: Crystal structure of lysoplasmalogen specific phopholipase D, F21... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ymq
TitleCrystal structure of lysoplasmalogen specific phopholipase D, F211L mutant
ComponentsLysoplasmalogenase
KeywordsHYDROLASE / phospholipase D / lysoplasmalogen / F211L murant
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / Lysoplasmalogenase
Function and homology information
Biological speciesThermocrispum sp. RD004668 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Sugimori, D. / Shirouzu, M. / Hamana, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2022
Title: Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668.
Authors: Hamana, H. / Yasutake, Y. / Kato-Murayama, M. / Hosaka, T. / Shirouzu, M. / Sakasegawa, S.I. / Sugimori, D. / Murayama, K.
History
DepositionJul 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysoplasmalogenase
B: Lysoplasmalogenase
C: Lysoplasmalogenase
D: Lysoplasmalogenase
E: Lysoplasmalogenase
F: Lysoplasmalogenase
G: Lysoplasmalogenase
H: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)275,3448
Polymers275,3448
Non-polymers00
Water11,187621
1
A: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Lysoplasmalogenase


Theoretical massNumber of molelcules
Total (without water)34,4181
Polymers34,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.570, 93.750, 147.810
Angle α, β, γ (deg.)90.000, 90.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Lysoplasmalogenase


Mass: 34418.059 Da / Num. of mol.: 8 / Mutation: F211L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum sp. RD004668 (bacteria) / Gene: lyspls / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4VTN7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG3350, Na Citrate, Ammonium Acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→47.94 Å / Num. obs: 129674 / % possible obs: 94.4 % / Redundancy: 3.5 % / CC1/2: 0.987 / Net I/σ(I): 5.7
Reflection shellResolution: 2.29→2.43 Å / Num. unique obs: 21072 / CC1/2: 0.549

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pz0

2pz0


Resolution: 2.29→46.88 Å / SU ML: 0.3378 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.55 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2373 6577 5.08 %
Rwork0.1849 122898 -
obs0.1875 129475 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.44 Å2
Refinement stepCycle: LAST / Resolution: 2.29→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18551 0 0 621 19172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008219031
X-RAY DIFFRACTIONf_angle_d0.945925974
X-RAY DIFFRACTIONf_chiral_restr0.0532897
X-RAY DIFFRACTIONf_plane_restr0.00723462
X-RAY DIFFRACTIONf_dihedral_angle_d3.148511520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.32362180.29384029X-RAY DIFFRACTION93.46
2.32-2.340.33982350.28534051X-RAY DIFFRACTION93.77
2.34-2.370.34952230.28084067X-RAY DIFFRACTION94.26
2.37-2.40.30992030.25734087X-RAY DIFFRACTION94.51
2.4-2.430.31411880.2554075X-RAY DIFFRACTION93.77
2.43-2.470.31622320.24944076X-RAY DIFFRACTION94.1
2.47-2.50.31091890.25154067X-RAY DIFFRACTION93.68
2.5-2.540.30972140.25144036X-RAY DIFFRACTION93.18
2.54-2.580.32062420.24533835X-RAY DIFFRACTION90.56
2.58-2.620.31522030.23923931X-RAY DIFFRACTION90.52
2.62-2.670.32182010.2364119X-RAY DIFFRACTION94.45
2.67-2.720.27062280.22864145X-RAY DIFFRACTION96.07
2.72-2.770.28882120.2284156X-RAY DIFFRACTION96.06
2.77-2.820.29382010.24044172X-RAY DIFFRACTION95.73
2.82-2.890.31112290.24624141X-RAY DIFFRACTION96.02
2.89-2.950.32852310.22964159X-RAY DIFFRACTION95.83
2.95-3.030.26172380.2214177X-RAY DIFFRACTION96.04
3.03-3.110.28891990.2154149X-RAY DIFFRACTION95.5
3.11-3.20.27242160.2164131X-RAY DIFFRACTION95.64
3.2-3.30.26452360.21224143X-RAY DIFFRACTION95.34
3.3-3.420.28212540.21064058X-RAY DIFFRACTION95.15
3.42-3.560.26272410.19484162X-RAY DIFFRACTION95.3
3.56-3.720.19961880.17714191X-RAY DIFFRACTION95.55
3.72-3.920.21852180.16584139X-RAY DIFFRACTION95.05
3.92-4.160.21872220.15824083X-RAY DIFFRACTION94
4.16-4.480.2062030.14614107X-RAY DIFFRACTION93.65
4.48-4.930.17071970.13123957X-RAY DIFFRACTION90.66
4.93-5.640.18822420.13914177X-RAY DIFFRACTION95.42
5.64-7.110.19292450.15174186X-RAY DIFFRACTION95.56
7.11-46.880.15662290.13574092X-RAY DIFFRACTION91.01

+
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