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- PDB-4b5n: Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) -

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Basic information

Entry
Database: PDB / ID: 4b5n
TitleCrystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4)
ComponentsOXIDOREDUCTASE, FMN-BINDING
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 / FLAVIN MONONUCLEOTIDE / NAD(P)H:flavin oxidoreductase Sye4
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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
DepositionAug 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: 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 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OXIDOREDUCTASE, FMN-BINDING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8403
Polymers39,1291
Non-polymers7112
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.230, 54.810, 103.550
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 OXIDOREDUCTASE, FMN-BINDING / / SHEWANELLA YELLOW ENZYME 4


Mass: 39129.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA ONEIDENSIS MR-1 (bacteria) / Plasmid: PACYC-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EBV3, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#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.: 493 / 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: 1.91 Å3/Da / Density % sol: 35.5 % / Description: NONE
Crystal growpH: 6.3 / Details: 1.6M SODIUM CITRATE TRIBASIC DIHYDRATE, PH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.85
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 120389 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 9.54 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.3
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GOU

2gou


Resolution: 1.1→48.442 Å / SU ML: 0.08 / σ(F): 1.99 / Phase error: 12.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1405 1411 1.2 %
Rwork0.127 --
obs0.1272 120388 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 12.4 Å2
Refinement stepCycle: LAST / Resolution: 1.1→48.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 49 493 3291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093077
X-RAY DIFFRACTIONf_angle_d1.4264222
X-RAY DIFFRACTIONf_dihedral_angle_d13.7641186
X-RAY DIFFRACTIONf_chiral_restr0.084469
X-RAY DIFFRACTIONf_plane_restr0.01553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.13930.17661420.141811818X-RAY DIFFRACTION100
1.1393-1.1850.15861470.128611789X-RAY DIFFRACTION100
1.185-1.23890.14231210.123311832X-RAY DIFFRACTION100
1.2389-1.30420.15751370.118811856X-RAY DIFFRACTION100
1.3042-1.38590.1441450.10811809X-RAY DIFFRACTION100
1.3859-1.49290.1311490.106811895X-RAY DIFFRACTION100
1.4929-1.64320.13781390.104511807X-RAY DIFFRACTION99
1.6432-1.8810.11791360.112711943X-RAY DIFFRACTION100
1.881-2.36980.12831550.124311900X-RAY DIFFRACTION98
2.3698-48.48950.14881400.145312328X-RAY DIFFRACTION99

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