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- PDB-5k0r: Crystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4) -

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Basic information

Entry
Database: PDB / ID: 5k0r
TitleCrystal structure of reduced Shewanella Yellow Enzyme 4 (SYE4)
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
Octadecane / Chem-FNR / NAD(P)H:flavin oxidoreductase Sye4
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsElegheert, J. / Brige, A. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Belgium
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 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,8423
Polymers39,1291
Non-polymers7132
Water9,152508
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-5 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.220, 54.780, 103.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Plasmid: PACYC-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8EBV3, flavin reductase (NADPH)
#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical ChemComp-8K6 / Octadecane / N-Octadecane / Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.81 % / 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

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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: 1.45→25 Å / Num. obs: 52643 / % possible obs: 98.8 % / Redundancy: 7.2 % / Rsym value: 0.059 / Net I/σ(I): 29.1
Reflection shellResolution: 1.45→1.49 Å / Rsym value: 0.542

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Processing

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

4b5n


Resolution: 1.45→24.256 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 15.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 1945 3.7 %
Rwork0.1482 --
obs0.1493 52636 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→24.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 49 508 3252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052910
X-RAY DIFFRACTIONf_angle_d1.0653978
X-RAY DIFFRACTIONf_dihedral_angle_d14.0291089
X-RAY DIFFRACTIONf_chiral_restr0.061442
X-RAY DIFFRACTIONf_plane_restr0.008517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.27721330.24213554X-RAY DIFFRACTION98
1.4863-1.52640.24511300.22473533X-RAY DIFFRACTION98
1.5264-1.57140.2381520.2073540X-RAY DIFFRACTION98
1.5714-1.62210.23191370.19063559X-RAY DIFFRACTION98
1.6221-1.680.19831240.17213580X-RAY DIFFRACTION98
1.68-1.74730.19251420.15753587X-RAY DIFFRACTION99
1.7473-1.82680.19861620.14893570X-RAY DIFFRACTION99
1.8268-1.9230.1681240.14153592X-RAY DIFFRACTION99
1.923-2.04350.16751450.13613619X-RAY DIFFRACTION99
2.0435-2.20110.17641260.133638X-RAY DIFFRACTION99
2.2011-2.42250.19161400.13043655X-RAY DIFFRACTION99
2.4225-2.77260.16691460.13333665X-RAY DIFFRACTION99
2.7726-3.49150.15731350.13173726X-RAY DIFFRACTION99
3.4915-24.25930.14841490.13713873X-RAY DIFFRACTION99

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