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- PDB-3txz: OYE1-W116Q complexed with R-carvone -

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Basic information

Entry
Database: PDB / ID: 3txz
TitleOYE1-W116Q complexed with R-carvone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / Enantioselectivity / Alkene Reductase / Enone reductase / OYE Old yellow enzyme / TIM Barrel / NAD(P)H Oxidoreductase / Flavin mononucleotide / Nicotinamide adenine dinucleotide
Function / homology
Function and homology information


NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding / apoptotic process
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
Chem-07V / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSullivan, B. / Pompeu, Y.A. / Stewart, J.D.
CitationJournal: ACS CATALYSIS / Year: 2013
Title: X‑ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase
Authors: Pompeu, Y.A. / Sullivan, B. / Stewart, J.D.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6444
Polymers45,0141
Non-polymers6313
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.362, 141.362, 42.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-852-

HOH

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Components

#1: Protein NADPH dehydrogenase 1 / Old yellow enzyme 1


Mass: 45013.562 Da / Num. of mol.: 1 / Mutation: W116Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02899, 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-07V / (5R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one / R-carvone


Mass: 150.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 15, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. obs: 48165 / % possible obs: 98 % / Observed criterion σ(I): 3 / Rsym value: 0.065
Reflection shellHighest resolution: 1.7 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 41 / Rsym value: 0.58 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
PHENIX(phenix.refine: 1.7.2_862)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45 Å / SU ML: 0.37 / σ(F): 1.37 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 4817 10 %
Rwork0.161 --
obs0.1635 48163 99.99 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.915 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7283 Å2-0 Å20 Å2
2---2.7283 Å2-0 Å2
3---5.4565 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 43 368 3584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063380
X-RAY DIFFRACTIONf_angle_d1.0054601
X-RAY DIFFRACTIONf_dihedral_angle_d14.6811273
X-RAY DIFFRACTIONf_chiral_restr0.076476
X-RAY DIFFRACTIONf_plane_restr0.004605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7003-1.71960.30741600.24011441X-RAY DIFFRACTION100
1.7196-1.73990.23441560.21071398X-RAY DIFFRACTION100
1.7399-1.76110.25541570.2061414X-RAY DIFFRACTION100
1.7611-1.78340.21111600.19061441X-RAY DIFFRACTION100
1.7834-1.80690.23841540.18531393X-RAY DIFFRACTION100
1.8069-1.83160.20931590.17341420X-RAY DIFFRACTION100
1.8316-1.85780.20221600.16631451X-RAY DIFFRACTION100
1.8578-1.88550.2031550.15081399X-RAY DIFFRACTION100
1.8855-1.9150.20641600.15851431X-RAY DIFFRACTION100
1.915-1.94640.20171600.15341445X-RAY DIFFRACTION100
1.9464-1.97990.18171550.1531397X-RAY DIFFRACTION100
1.9799-2.01590.18951610.1531448X-RAY DIFFRACTION100
2.0159-2.05470.20141580.15211417X-RAY DIFFRACTION100
2.0547-2.09670.18881570.15221419X-RAY DIFFRACTION100
2.0967-2.14220.19541630.14871458X-RAY DIFFRACTION100
2.1422-2.19210.1751560.14661407X-RAY DIFFRACTION100
2.1921-2.24690.17061630.14311468X-RAY DIFFRACTION100
2.2469-2.30760.20491560.15231406X-RAY DIFFRACTION100
2.3076-2.37560.17771610.15071443X-RAY DIFFRACTION100
2.3756-2.45220.17081580.14711431X-RAY DIFFRACTION100
2.4522-2.53990.17971630.14941460X-RAY DIFFRACTION100
2.5399-2.64160.18291610.14751451X-RAY DIFFRACTION100
2.6416-2.76180.17721600.14181433X-RAY DIFFRACTION100
2.7618-2.90740.19291610.15181456X-RAY DIFFRACTION100
2.9074-3.08950.1711640.15591467X-RAY DIFFRACTION100
3.0895-3.3280.18521620.15121464X-RAY DIFFRACTION100
3.328-3.66280.1551640.15221474X-RAY DIFFRACTION100
3.6628-4.19260.16951660.15231492X-RAY DIFFRACTION100
4.1926-5.28130.15841690.15991518X-RAY DIFFRACTION100
5.2813-50.00060.23451780.21761604X-RAY DIFFRACTION100

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