[English] 日本語
Yorodumi
- PDB-7e2a: GDPD mutant from Pyrococcus furiosus DSM 3638 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e2a
TitleGDPD mutant from Pyrococcus furiosus DSM 3638
ComponentsGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Glycerophosphate phosphodiesterase / Hydrolysis / glycerophosphorylcholine / lysophosphorylcholine
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / Glycerophosphodiester phosphodiesterase
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWang, Y.H. / Wang, J. / Wang, F.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725022 China
National Natural Science Foundation of China (NSFC)31972014 China
CitationJournal: To Be Published
Title: Crystal structure of glycerophoshphodiester phospodiesterase D60A mutant from Pyrococcus furiosus DSM
Authors: Wang, Y.H. / Wang, J. / Wang, F.H.
History
DepositionFeb 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: 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: Glycerophosphodiester phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)29,3741
Polymers29,3741
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11150 Å2
Unit cell
Length a, b, c (Å)46.890, 69.600, 89.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Glycerophosphodiester phosphodiesterase


Mass: 29374.217 Da / Num. of mol.: 1 / Mutation: D60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hepes (pH 7.5), 25% w/v PEG3350, 0.2M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97921 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.08→23.45 Å / Num. obs: 18312 / % possible obs: 99.9 % / Observed criterion σ(I): 2.7 / Redundancy: 12.9 % / Biso Wilson estimate: 39.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Net I/σ(I): 14.7
Reflection shellResolution: 2.08→2.13 Å / Num. unique obs: 1340 / CC1/2: 0.831

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OEC

4oec


Resolution: 2.08→23.45 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5643
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 912 4.99 %
Rwork0.185 17349 -
obs0.1873 18261 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.98 Å2
Refinement stepCycle: LAST / Resolution: 2.08→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 0 68 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412072
X-RAY DIFFRACTIONf_angle_d1.22962794
X-RAY DIFFRACTIONf_chiral_restr0.0645320
X-RAY DIFFRACTIONf_plane_restr0.0101353
X-RAY DIFFRACTIONf_dihedral_angle_d6.0588274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.190.29521340.24662432X-RAY DIFFRACTION100
2.19-2.330.30011290.2432432X-RAY DIFFRACTION99.81
2.33-2.510.24081360.20932429X-RAY DIFFRACTION100
2.51-2.760.28331240.20362465X-RAY DIFFRACTION99.96
2.76-3.160.2831330.20652470X-RAY DIFFRACTION100
3.16-3.970.22371160.1792503X-RAY DIFFRACTION100
3.97-23.450.18621400.1582618X-RAY DIFFRACTION99.71

+
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