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- PDB-4awu: Crystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE... -

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Basic information

Entry
Database: PDB / ID: 4awu
TitleCrystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE1) M25L mutant in complex with para-chlorophenol
ComponentsOXIDOREDUCTASE, FMN-BINDING
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / 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
4-chlorophenol / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase Sye1
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsElegheert, J. / Brige, A. / Savvides, S.N.
CitationJournal: To be Published
Title: Modulation of Isoalloxazine Ring Planarity Influences Fmn Electronic Properties in Old Yellow Enzymes
Authors: Elegheert, J. / Pauwels, E. / Wille, G. / Brige, A. / Savvides, S.N.
History
DepositionJun 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 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:
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Assembly

Deposited unit
A: OXIDOREDUCTASE, FMN-BINDING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9067
Polymers39,6141
Non-polymers1,2936
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.820, 83.670, 87.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein OXIDOREDUCTASE, FMN-BINDING /


Mass: 39613.543 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Strain: MR-1 / Plasmid: PACYC-DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EEC8, NADPH dehydrogenase

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Non-polymers , 5 types, 411 molecules

#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-4CH / 4-chlorophenol / 4-Chlorophenol


Mass: 128.556 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5ClO
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 25 TO LEU

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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: 2.22 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 8.2
Details: 100 MM TRIS PH 8.2, 1.65 M (NH4)2SO4, 2 % PEG400 AND 0.25 % (W/V) BETA-OCTYL GLUCOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015
DetectorType: MARRESEARCH SX-165 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.7→42 Å / Num. obs: 40083 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 16.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AWS
Resolution: 1.69→41.997 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 2007 5 %
Rwork0.1692 --
obs0.1704 40076 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Refinement stepCycle: LAST / Resolution: 1.69→41.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 84 405 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042994
X-RAY DIFFRACTIONf_angle_d0.9014088
X-RAY DIFFRACTIONf_dihedral_angle_d14.5031118
X-RAY DIFFRACTIONf_chiral_restr0.05445
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6902-1.73240.27081360.22982637X-RAY DIFFRACTION98
1.7324-1.77930.261420.22492697X-RAY DIFFRACTION100
1.7793-1.83160.26051410.222673X-RAY DIFFRACTION100
1.8316-1.89070.32581410.25862680X-RAY DIFFRACTION99
1.8907-1.95830.24271410.21832664X-RAY DIFFRACTION100
1.9583-2.03670.24341440.1842695X-RAY DIFFRACTION100
2.0367-2.12940.18681420.17652718X-RAY DIFFRACTION100
2.1294-2.24170.21991430.17942704X-RAY DIFFRACTION100
2.2417-2.38210.18961420.16412711X-RAY DIFFRACTION100
2.3821-2.5660.18811430.16242720X-RAY DIFFRACTION100
2.566-2.82420.1521450.15522751X-RAY DIFFRACTION100
2.8242-3.23270.17261450.15072735X-RAY DIFFRACTION100
3.2327-4.07240.17551480.1432779X-RAY DIFFRACTION100
4.0724-42.01040.15121540.15332905X-RAY DIFFRACTION99

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