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

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Basic information

Entry
Database: PDB / ID: 4aws
TitleCrystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE1) M25L mutant
ComponentsSYE1
KeywordsOXIDOREDUCTASE / COFACTOR-BINDING
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
ethyl hydrogen carbonate / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase Sye1
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 1.1May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: SYE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2817
Polymers39,7001
Non-polymers1,5826
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.560, 83.900, 87.760
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 / Sugars , 2 types, 3 molecules A

#1: Protein SYE1 / OXIDOREDUCTASE / FMN-BINDING


Mass: 39699.629 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL T2 IS INVOLVED IN AN N, O FIVE RING ACETAL BY REACTION WITH HO-CH2-CH2-O-CH2-CHO, A PEG400 BREAKDOWN PRODUCT.
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
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 566 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
#5: Chemical ChemComp-01F / ethyl hydrogen carbonate


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFMN IS THE CATALYTIC COFACTOR FOR THE PROTEIN.
Sequence detailsM25L MUTATION TO INFLUENCE THE FMN PLANARITY.

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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: 2.26 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: 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→45 Å / Num. obs: 192252 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 1→1.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GOU

2gou


Resolution: 1→45 Å / Num. parameters: 33010 / Num. restraintsaints: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1352 1923 1 %RANDOM
obs0.1155 -98.4 %-
all-190328 --
Refine analyzeNum. disordered residues: 38 / Occupancy sum hydrogen: 2835.25 / Occupancy sum non hydrogen: 3443.67
Refinement stepCycle: LAST / Resolution: 1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 106 562 3459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.0043
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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