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- PDB-5k1q: Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) i... -

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Basic information

Entry
Database: PDB / ID: 5k1q
TitleCrystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) in complex with p-methylphenol
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 / P-CRESOL / NAD(P)H:flavin oxidoreductase Sye4
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)40,2348
Polymers39,1291
Non-polymers1,1057
Water8,395466
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-19 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.260, 54.790, 103.670
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)
Strain: MR-1 / Gene: sye4, SO_3392 / Plasmid: PACYC-DUET / 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-PCR / P-CRESOL


Mass: 108.138 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 1.9 Å3/Da / Density % sol: 35.15 % / 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 8, 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: 42707 / % possible obs: 97.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.8
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.44

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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: 1.55→24.263 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.72
RfactorNum. reflection% reflection
Rfree0.1717 2073 4.85 %
Rwork0.1365 --
obs0.1382 42706 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→24.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 79 466 3240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082924
X-RAY DIFFRACTIONf_angle_d1.1763991
X-RAY DIFFRACTIONf_dihedral_angle_d12.7821072
X-RAY DIFFRACTIONf_chiral_restr0.07437
X-RAY DIFFRACTIONf_plane_restr0.007517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58610.31161460.2752620X-RAY DIFFRACTION95
1.5861-1.62570.26041260.24092619X-RAY DIFFRACTION95
1.6257-1.66970.23081300.21352667X-RAY DIFFRACTION97
1.6697-1.71880.2281350.18042716X-RAY DIFFRACTION99
1.7188-1.77420.20061450.15372709X-RAY DIFFRACTION99
1.7742-1.83760.19811570.14582715X-RAY DIFFRACTION99
1.8376-1.91120.16841250.13132727X-RAY DIFFRACTION98
1.9112-1.99810.1721490.12552717X-RAY DIFFRACTION98
1.9981-2.10340.17221320.1152735X-RAY DIFFRACTION98
2.1034-2.23510.15651250.11142699X-RAY DIFFRACTION98
2.2351-2.40750.16111380.10892727X-RAY DIFFRACTION98
2.4075-2.64950.13671350.11242733X-RAY DIFFRACTION97
2.6495-3.03230.13811560.11462713X-RAY DIFFRACTION97
3.0323-3.8180.14691340.112727X-RAY DIFFRACTION96
3.818-24.26640.15571400.13952809X-RAY DIFFRACTION94

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