[English] 日本語
Yorodumi
- PDB-5k1u: Crystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4) in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k1u
TitleCrystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4) in complex with the hydride Meisenheimer complex of trinitrophenol
ComponentsNAD(P)H:flavin oxidoreductase Sye4
KeywordsOXIDOREDUCTASE / COFACTOR-BINDING
Function / homology
Function and homology information


flavin reductase (NADPH) / riboflavin reductase (NADPH) activity / FMN binding / cytosol
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
FLAVIN MONONUCLEOTIDE / PICRIC ACID / NAD(P)H:flavin oxidoreductase Sye4
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsElegheert, J. / Brige, A. / Savvides, S.N.
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.
Authors: Elegheert, J. / Brige, A. / Van Beeumen, J. / Savvides, S.N.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P)H:flavin oxidoreductase Sye4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0444
Polymers39,1291
Non-polymers9153
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-22 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.430, 54.470, 105.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NAD(P)H:flavin oxidoreductase Sye4


Mass: 39129.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Gene: sye4, SO_3392 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EBV3, flavin reductase (NADPH)
#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-TNF / PICRIC ACID / 2,4,6-TRINITROPHENOL


Mass: 229.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H3N3O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 1.85 Å3/Da / Density % sol: 33.42 % / Description: clothes pin
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 1.6 M sodium citrate tribasic dihydrate pH 6.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 42455 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.9
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.551

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5N

4b5n


Resolution: 1.551→24.189 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 14.15
RfactorNum. reflection% reflection
Rfree0.1657 2063 4.86 %
Rwork0.1303 --
obs0.132 42454 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.551→24.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 63 513 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062917
X-RAY DIFFRACTIONf_angle_d1.0863992
X-RAY DIFFRACTIONf_dihedral_angle_d13.5671060
X-RAY DIFFRACTIONf_chiral_restr0.067436
X-RAY DIFFRACTIONf_plane_restr0.006525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5514-1.58750.24671260.22182538X-RAY DIFFRACTION96
1.5875-1.62720.22461460.20032668X-RAY DIFFRACTION100
1.6272-1.67120.21821270.18112678X-RAY DIFFRACTION100
1.6712-1.72040.24831340.16442668X-RAY DIFFRACTION100
1.7204-1.77590.1881350.1512654X-RAY DIFFRACTION100
1.7759-1.83930.1651370.13832672X-RAY DIFFRACTION100
1.8393-1.91290.17211440.1312680X-RAY DIFFRACTION100
1.9129-20.18871520.12592681X-RAY DIFFRACTION100
2-2.10530.15351270.11922715X-RAY DIFFRACTION100
2.1053-2.23720.17211120.10932700X-RAY DIFFRACTION100
2.2372-2.40970.15011460.10912700X-RAY DIFFRACTION100
2.4097-2.6520.15251470.11572721X-RAY DIFFRACTION100
2.652-3.03510.14721450.11652722X-RAY DIFFRACTION100
3.0351-3.82150.13671470.10952745X-RAY DIFFRACTION99
3.8215-24.19170.14651380.13152849X-RAY DIFFRACTION98

+
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