[English] 日本語
Yorodumi
- PDB-9eno: Crystal structure of ComplemEnT1.4 (CEnT1.4), an engineered photo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eno
TitleCrystal structure of ComplemEnT1.4 (CEnT1.4), an engineered photoenzyme for selective [2+2]-cycloadditions
ComponentsDiisopropyl-fluorophosphatase
KeywordsBIOSYNTHETIC PROTEIN / photoenzyme / [2+2]-cyclase / artificial enzyme
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLoligo vulgaris (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHardy, F.J. / Crawshaw, R.C. / Green, A.P.
Funding supportEuropean Union, United Kingdom, France, 6items
OrganizationGrant numberCountry
European Research Council (ERC)757991European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Human Frontier Science Program (HFSP)RGP0004/2022 France
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S507969/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/W524347/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Photosensitizer Repositioning Affords an Enantiocomplementary Enzyme for [2 + 2]-Cycloadditions.
Authors: Sun, C. / Kohn, A.R. / Smithson, R. / Hardy, F.J. / Trimble, J.S. / Cao, Y. / Johannissen, L.O. / Hay, S. / Crawshaw, R. / Green, A.P.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diisopropyl-fluorophosphatase
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6587
Polymers73,1712
Non-polymers4875
Water8,089449
1
A: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7103
Polymers36,5851
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9484
Polymers36,5851
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.970, 73.917, 74.870
Angle α, β, γ (deg.)90.000, 92.850, 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 Diisopropyl-fluorophosphatase / DFPase


Mass: 36585.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, EC: 3.1.8.2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M ammonium sulphate, 0.2 M sodium chloride, 0.1 M sodium cacodylate
Temp details: humidified cabinet

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→51.91 Å / Num. obs: 59053 / % possible obs: 98.97 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1659 / Net I/σ(I): 6.98
Reflection shellResolution: 1.73→1.792 Å / Rmerge(I) obs: 2.152 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 5851 / CC1/2: 0.459 / % possible all: 92.25

-
Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→51.91 Å / SU ML: 0.2353 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 2081 3.55 %
Rwork0.1812 56480 -
obs0.1828 58561 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.73→51.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 32 449 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675010
X-RAY DIFFRACTIONf_angle_d0.96326791
X-RAY DIFFRACTIONf_chiral_restr0.0589715
X-RAY DIFFRACTIONf_plane_restr0.0107897
X-RAY DIFFRACTIONf_dihedral_angle_d11.1591696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.31381270.31033313X-RAY DIFFRACTION88.07
1.77-1.810.34351120.29873762X-RAY DIFFRACTION98.35
1.81-1.860.35271100.28593779X-RAY DIFFRACTION99.01
1.86-1.920.29071440.27943771X-RAY DIFFRACTION99.16
1.92-1.980.27411270.25023758X-RAY DIFFRACTION99.64
1.98-2.050.24441310.22523803X-RAY DIFFRACTION99.8
2.05-2.130.29641640.20313767X-RAY DIFFRACTION99.87
2.13-2.230.21771570.19313769X-RAY DIFFRACTION99.57
2.23-2.350.25051720.18643762X-RAY DIFFRACTION99.85
2.35-2.490.24231700.17673773X-RAY DIFFRACTION99.95
2.49-2.690.28051540.17753801X-RAY DIFFRACTION99.97
2.69-2.960.23411170.17553836X-RAY DIFFRACTION100
2.96-3.380.21261040.16053853X-RAY DIFFRACTION99.97
3.38-4.260.16751360.13983845X-RAY DIFFRACTION100
4.26-51.910.17911560.15493888X-RAY DIFFRACTION99.9

+
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