[English] 日本語
Yorodumi
- PDB-3tx9: OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tx9
TitleOYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / OYE / Old yellow enzyme / flavin mononucleotide / NADPH / Baylis-hillman / alkene reductase / enone reductase / TIM barrel / NADPH Oxidoreductase
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-(hydroxymethyl)cyclopent-2-en-1-one / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: To be Published
Title: Studies of Enantioselectivity in OYE1
Authors: Pompeu, Y.A. / Stewart, J.D.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6644
Polymers45,0721
Non-polymers5933
Water4,071226
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3298
Polymers90,1432
Non-polymers1,1866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)141.188, 141.188, 42.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 45071.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3RN / 2-(hydroxymethyl)cyclopent-2-en-1-one


Mass: 112.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M MgCl2, 0.1M HEPES, 35-40% PEG400, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 15, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. all: 30521 / Num. obs: 29638 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 4.2 %
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 18 / Num. unique all: 29638 / Rsym value: 0.58 / % possible all: 98

-
Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.2_863)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA

1oya


Resolution: 1.999→44.648 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 2959 10 %random
Rwork0.1824 ---
obs0.1859 29586 99.18 %-
all-30521 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.704 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3266 Å2-0 Å20 Å2
2---1.3266 Å20 Å2
3---2.6531 Å2
Refinement stepCycle: LAST / Resolution: 1.999→44.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 40 226 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083330
X-RAY DIFFRACTIONf_angle_d1.0624524
X-RAY DIFFRACTIONf_dihedral_angle_d14.7161232
X-RAY DIFFRACTIONf_chiral_restr0.076467
X-RAY DIFFRACTIONf_plane_restr0.009592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.03150.26241380.21851246X-RAY DIFFRACTION98
2.0315-2.06650.3241370.22361228X-RAY DIFFRACTION99
2.0665-2.10410.23491370.20771234X-RAY DIFFRACTION99
2.1041-2.14460.24451390.2031255X-RAY DIFFRACTION100
2.1446-2.18830.2571370.19891229X-RAY DIFFRACTION99
2.1883-2.23590.25521390.19721250X-RAY DIFFRACTION98
2.2359-2.28790.25131370.19321237X-RAY DIFFRACTION99
2.2879-2.34510.24341390.18911248X-RAY DIFFRACTION99
2.3451-2.40850.26361380.18731244X-RAY DIFFRACTION99
2.4085-2.47940.21561380.18061234X-RAY DIFFRACTION98
2.4794-2.55940.22571370.1781242X-RAY DIFFRACTION99
2.5594-2.65090.23591420.18111270X-RAY DIFFRACTION99
2.6509-2.7570.22811390.17321255X-RAY DIFFRACTION100
2.757-2.88250.22421420.17981284X-RAY DIFFRACTION100
2.8825-3.03440.20371420.17761268X-RAY DIFFRACTION100
3.0344-3.22450.20651410.18461278X-RAY DIFFRACTION100
3.2245-3.47330.19261430.1751283X-RAY DIFFRACTION100
3.4733-3.82270.20361450.16071302X-RAY DIFFRACTION100
3.8227-4.37550.20451440.1611302X-RAY DIFFRACTION100
4.3755-5.5110.18741480.17421328X-RAY DIFFRACTION99
5.511-44.65870.21211570.21481410X-RAY DIFFRACTION99

+
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