[English] 日本語
Yorodumi
- PDB-7qfx: Crystal structure of Old Yellow Enzyme AnOYE8 from Aspergillus niger -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qfx
TitleCrystal structure of Old Yellow Enzyme AnOYE8 from Aspergillus niger
ComponentsNADH-dependent flavin oxidoreductase
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / Ene-reductase
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-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
FLAVIN MONONUCLEOTIDE / NADH-dependent flavin oxidoreductase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRobescu, M.S. / Loprete, G. / Vascon, F. / Gasparotto, M. / Filippini, F. / Bergantino, E. / Cendron, L.
Funding support1items
OrganizationGrant numberCountry
Other government
Citation
Journal: Int J Mol Sci / Year: 2022
Title: The Family Keeps on Growing: Four Novel Fungal OYEs Characterized.
Authors: Robescu, M.S. / Loprete, G. / Gasparotto, M. / Vascon, F. / Filippini, F. / Cendron, L. / Bergantino, E.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: NADH-dependent flavin oxidoreductase
C: NADH-dependent flavin oxidoreductase
E: NADH-dependent flavin oxidoreductase
G: NADH-dependent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,96813
Polymers183,6404
Non-polymers2,3289
Water1,53185
1
B: NADH-dependent flavin oxidoreductase
C: NADH-dependent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9256
Polymers91,8202
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-79 kcal/mol
Surface area27170 Å2
MethodPISA
2
E: NADH-dependent flavin oxidoreductase
G: NADH-dependent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0437
Polymers91,8202
Non-polymers1,2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-89 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.533, 65.388, 181.417
Angle α, β, γ (deg.)90.000, 107.760, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
NADH-dependent flavin oxidoreductase


Mass: 45910.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: M747DRAFT_320366 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A370CG11
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % w/v PEG 5000 MME, 0.1 M MES pH 6.5, 0.2 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→39.98 Å / Num. obs: 43316 / % possible obs: 97 % / Redundancy: 4.8 % / Biso Wilson estimate: 52.61 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3 / Num. unique obs: 4327 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LNJ

5lnj


Resolution: 2.8→39.95 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 --RANDOM
Rwork0.2415 ---
obs-43315 95.99 %-
Displacement parametersBiso max: 151.91 Å2 / Biso mean: 72.6487 Å2 / Biso min: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12554 0 152 85 12791

+
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