[English] 日本語
Yorodumi
- PDB-8sfk: Crystal structure of the engineered SsoPox variant IVE2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sfk
TitleCrystal structure of the engineered SsoPox variant IVE2
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / Lactonase / quorum sensing / phosphotriesterase / arylesterase
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolase
Similarity search - Domain/homology
: / : / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJacquet, P. / Billot, R. / Shimon, A. / Hoekstra, N. / Bergonzi, C. / Jenks, A. / Daude, D. / Elias, M.H.
Funding support France, United States, 5items
OrganizationGrant numberCountry
Other governmentDGA France
Agence Nationale de la Recherche (ANR)10-IAHU-03 France
Other governmentMndrive United States
Other governmentBiotechnology Institute United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133487 United States
CitationJournal: To Be Published
Title: Changes in Active Site Loops Conformation Relates to a Transition from Lactonase to Phosphotriesterase
Authors: Jacquet, P. / Billot, R. / Shimon, A. / Hoekstra, N. / Bergonzi, C. / Jenks, A. / Chabriere, E. / Daude, D. / Elias, M.H.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7384
Polymers35,5311
Non-polymers2073
Water8,359464
1
D: Aryldialkylphosphatase
hetero molecules

D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4758
Polymers71,0622
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4610 Å2
ΔGint-72 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.060, 74.670, 137.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Aryldialkylphosphatase / Paraoxonase / SsoPox / Phosphotriesterase-like lactonase


Mass: 35530.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: php, SSO2522 / Variant: IVE2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q97VT7, aryldialkylphosphatase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG 8000 and Tris-HCl buffer (pH 8.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96802 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96802 Å / Relative weight: 1
ReflectionResolution: 1.4→49.477 Å / Num. obs: 67061 / % possible obs: 100 % / Redundancy: 4.34 % / CC1/2: 1 / Rrim(I) all: 0.063 / Net I/σ(I): 19.91
Reflection shellResolution: 1.4→1.5 Å / Num. unique obs: 12397 / CC1/2: 0.917 / Rrim(I) all: 0.633

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→49.477 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1693 3345 5 %
Rwork0.1354 --
obs0.1371 66910 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→49.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 8 464 2972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052725
X-RAY DIFFRACTIONf_angle_d0.8693705
X-RAY DIFFRACTIONf_dihedral_angle_d8.4431630
X-RAY DIFFRACTIONf_chiral_restr0.079413
X-RAY DIFFRACTIONf_plane_restr0.006488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.21781360.20022617X-RAY DIFFRACTION99
1.42-1.44120.19331370.16782586X-RAY DIFFRACTION99
1.4412-1.46370.22861380.16712636X-RAY DIFFRACTION99
1.4637-1.48770.18461360.15052581X-RAY DIFFRACTION100
1.4877-1.51340.21581380.1422651X-RAY DIFFRACTION100
1.5134-1.54090.17091370.1282599X-RAY DIFFRACTION100
1.5409-1.57050.15731390.12792620X-RAY DIFFRACTION99
1.5705-1.60260.15231390.12542627X-RAY DIFFRACTION100
1.6026-1.63750.15581370.12292613X-RAY DIFFRACTION100
1.6375-1.67550.17541370.12512627X-RAY DIFFRACTION100
1.6755-1.71750.1471410.12762666X-RAY DIFFRACTION100
1.7175-1.76390.16641370.12972604X-RAY DIFFRACTION100
1.7639-1.81580.17341380.12882621X-RAY DIFFRACTION100
1.8158-1.87440.14441400.12122654X-RAY DIFFRACTION100
1.8744-1.94140.15221390.12512635X-RAY DIFFRACTION100
1.9414-2.01910.16771400.12972660X-RAY DIFFRACTION100
2.0191-2.1110.14671400.13012648X-RAY DIFFRACTION100
2.111-2.22230.15431390.13272656X-RAY DIFFRACTION100
2.2223-2.36160.15621410.13192672X-RAY DIFFRACTION100
2.3616-2.54390.17131400.14162664X-RAY DIFFRACTION100
2.5439-2.79990.19211420.1462684X-RAY DIFFRACTION100
2.7999-3.2050.20451410.13872684X-RAY DIFFRACTION100
3.205-4.03760.17341440.1262733X-RAY DIFFRACTION100
4.0376-49.4770.15041490.14142827X-RAY DIFFRACTION100

+
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