[English] 日本語
Yorodumi
- PDB-8fw1: Gluconobacter Ene-Reductase (GluER) mutant - PagER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fw1
TitleGluconobacter Ene-Reductase (GluER) mutant - PagER
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / flavoprotein / 'ene'-reductase / photoenzyme
Function / homologyOxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / Alkene reductase
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDahagam, S. / Page, C. / Patterson, M.G. / Hyster, T.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127703-06 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141256 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2023
Title: Regioselective Radical Alkylation of Arenes Using Evolved Photoenzymes.
Authors: Page, C.G. / Cao, J. / Oblinsky, D.G. / MacMillan, S.N. / Dahagam, S. / Lloyd, R.M. / Charnock, S.J. / Scholes, G.D. / Hyster, T.K.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening.
Authors: Lynch, M.L. / Snell, M.E. / Potter, S.A. / Snell, E.H. / Bowman, S.E.J.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9046
Polymers118,5353
Non-polymers1,3693
Water8,431468
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9682
Polymers39,5121
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9682
Polymers39,5121
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9682
Polymers39,5121
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.165, 51.849, 144.935
Angle α, β, γ (deg.)90.510, 90.110, 114.860
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein N-ethylmaleimide reductase / PagER


Mass: 39511.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: nox / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1E8I9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris, 0.1 M potassium bromide, 20% w/v PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.5→45.51 Å / Num. obs: 205104 / % possible obs: 96.61 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.077 / Net I/σ(I): 7.9
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.309 / Num. unique obs: 10107 / Rpim(I) all: 0.239 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
DIALS3.12.1data reduction
PHENIX1.20.1_4487refinement
PHASER2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MYW

6myw


Resolution: 1.5→45.51 Å / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 25.5365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2728 2021 1 %
Rwork0.2675 201954 -
obs0.2792 203975 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8355 0 93 468 8916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038667
X-RAY DIFFRACTIONf_angle_d0.759811805
X-RAY DIFFRACTIONf_chiral_restr0.07641257
X-RAY DIFFRACTIONf_plane_restr0.00661560
X-RAY DIFFRACTIONf_dihedral_angle_d14.61463171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.42671330.426113475X-RAY DIFFRACTION88.62
1.54-1.580.40051290.400113924X-RAY DIFFRACTION91.61
1.58-1.630.34341540.373214276X-RAY DIFFRACTION94.16
1.63-1.680.31521380.343614346X-RAY DIFFRACTION94.94
1.68-1.740.32431440.316714379X-RAY DIFFRACTION94.79
1.74-1.810.25931200.299914426X-RAY DIFFRACTION95.21
1.81-1.890.25871480.281414499X-RAY DIFFRACTION95.59
1.89-1.990.24721460.258814493X-RAY DIFFRACTION95.46
1.99-2.110.2811510.267914545X-RAY DIFFRACTION96.14
2.11-2.280.27951490.273914631X-RAY DIFFRACTION96.28
2.28-2.510.30241410.27714670X-RAY DIFFRACTION96.79
2.51-2.870.27031520.267614750X-RAY DIFFRACTION97.24
2.87-3.610.25111420.265914702X-RAY DIFFRACTION97.08
3.61-45.510.26951410.241614871X-RAY DIFFRACTION98.13

+
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