[English] 日本語
Yorodumi
- PDB-4ync: OYE1 W116A COMPLEXED WITH (Z)-METHYL-3-CYANO-3-PHENYLACRYLATE IN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ync
TitleOYE1 W116A COMPLEXED WITH (Z)-METHYL-3-CYANO-3-PHENYLACRYLATE IN A NON PRODUCTIVE BINDING MODE
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / CATALYTIC ACTIVITY / FMN BINDING / OLD YELLOW ENZYME
Function / homology
Function and homology information


: / NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
methyl (2Z)-3-cyano-3-phenylprop-2-enoate / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsSantangelo, S. / Brenna, E. / Stewart, J.D. / Powell III, R.W.
CitationJournal: Adv.Synth.Catal. / Year: 2015
Title: Opposite Enantioselectivity in the Bioreduction of (Z)-beta-Aryl-beta-cyanoacrylates Mediated by the Tryptophan 116 Mutants of Old Yellow Enzyme 1: Synthetic Approach to (R)- and (S)-beta-Aryl-gamma-lactams
Authors: Brenna, E. / Crotti, M. / Gatti, F.G. / Monti, D. / Parmeggiani, F. / Powell III, R.W. / Santangelo, S. / Stewart, J.D.
History
DepositionMar 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2464
Polymers44,5671
Non-polymers6793
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-11 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.503, 141.503, 42.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-857-

HOH

21A-1028-

HOH

-
Components

#1: Protein NADPH dehydrogenase 1 / Old yellow enzyme 1


Mass: 44566.953 Da / Num. of mol.: 1 / Mutation: W116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET3b / Details (production host): pSA01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02899, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-4EG / methyl (2Z)-3-cyano-3-phenylprop-2-enoate


Mass: 187.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 0.2M MgCl2, 0.1M NaHEPES, 35% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.498→27.75 Å / Num. all: 70253 / Num. obs: 70253 / % possible obs: 99.76 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 29.05
Reflection shellResolution: 1.498→1.551 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 4.65 / % possible all: 99.39

-
Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOHKLSuite 0.95data reduction
SCALEPACKHKLSuite 0.95data scaling
PDB_EXTRACT3.15data extraction
PHENIX1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBU

4gbu


Resolution: 1.498→27.751 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 1998 2.84 %
Rwork0.1554 68241 -
obs0.1559 70239 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.04 Å2 / Biso mean: 18.988 Å2 / Biso min: 9.97 Å2
Refinement stepCycle: final / Resolution: 1.498→27.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 55 545 3751
Biso mean--17.79 29.39 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063406
X-RAY DIFFRACTIONf_angle_d1.1054646
X-RAY DIFFRACTIONf_chiral_restr0.081479
X-RAY DIFFRACTIONf_plane_restr0.005615
X-RAY DIFFRACTIONf_dihedral_angle_d13.9981297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4978-1.53520.22871400.18844790493099
1.5352-1.57670.21721410.17648094950100
1.5767-1.62310.19151400.173347884928100
1.6231-1.67550.20211410.162948114952100
1.6755-1.73540.22551420.160648314973100
1.7354-1.80490.19631420.164548254967100
1.8049-1.8870.18261410.158248364977100
1.887-1.98640.16411420.154848554997100
1.9864-2.11090.18371420.157348735015100
2.1109-2.27380.17741440.155648935037100
2.2738-2.50250.17071430.155748835026100
2.5025-2.86420.20431430.155449365079100
2.8642-3.60740.1471470.155549815128100
3.6074-27.75580.14891500.14315130528098

+
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