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- PDB-5k1k: Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) i... -

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Basic information

Entry
Database: PDB / ID: 5k1k
TitleCrystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) in complex with p-hydroxybenzaldehyde
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 / FLAVIN MONONUCLEOTIDE / P-HYDROXYBENZALDEHYDE / NAD(P)H:flavin oxidoreductase Sye4
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.301 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

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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)40,4508
Polymers39,1291
Non-polymers1,3217
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint14 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.090, 54.660, 103.750
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 / 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) / Gene: sye4, SO_3392 / Plasmid: PACYC-DUET / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8EBV3, flavin reductase (NADPH), 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-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


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


Mass: 18.015 Da / Num. of mol.: 499 / 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: 34.83 %
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: X13 / Wavelength: 0.8076 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8076 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 71727 / % possible obs: 97.3 % / Redundancy: 5.3 % / Rsym value: 0.107 / Net I/σ(I): 9.7
Reflection shellResolution: 1.3→1.35 Å / Rsym value: 0.597

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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: 1.301→19.444 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 12.2
RfactorNum. reflection% reflection
Rfree0.148 2014 2.81 %
Rwork0.1217 --
obs0.1225 71726 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.301→19.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 94 499 3288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013015
X-RAY DIFFRACTIONf_angle_d1.364121
X-RAY DIFFRACTIONf_dihedral_angle_d14.2251149
X-RAY DIFFRACTIONf_chiral_restr0.084448
X-RAY DIFFRACTIONf_plane_restr0.009536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.301-1.33360.23221240.19984101X-RAY DIFFRACTION82
1.3336-1.36960.20811400.16775027X-RAY DIFFRACTION100
1.3696-1.40990.18531400.1485024X-RAY DIFFRACTION100
1.4099-1.45540.16691550.13055029X-RAY DIFFRACTION100
1.4554-1.50740.14681610.12165027X-RAY DIFFRACTION100
1.5074-1.56770.1491450.11345046X-RAY DIFFRACTION100
1.5677-1.6390.15811360.11165031X-RAY DIFFRACTION100
1.639-1.72540.12881400.10695060X-RAY DIFFRACTION100
1.7254-1.83340.14881680.10595047X-RAY DIFFRACTION100
1.8334-1.97490.12911410.10395036X-RAY DIFFRACTION99
1.9749-2.17340.13811350.10485043X-RAY DIFFRACTION98
2.1734-2.48730.14771390.11165051X-RAY DIFFRACTION98
2.4873-3.13160.13741400.12075047X-RAY DIFFRACTION97
3.1316-19.44620.14131500.13355143X-RAY DIFFRACTION95

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