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- PDB-3tx9: OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone -

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Basic information

Entry
Database: PDB / ID: 3tx9
TitleOYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / OYE / Old yellow enzyme / flavin mononucleotide / NADPH / Baylis-hillman / alkene reductase / enone reductase / TIM barrel / NADPH Oxidoreductase
Function / homology
Function and homology information


: / NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding
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
2-(hydroxymethyl)cyclopent-2-en-1-one / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: To be Published
Title: Studies of Enantioselectivity in OYE1
Authors: Pompeu, Y.A. / Stewart, J.D.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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)45,6644
Polymers45,0721
Non-polymers5933
Water4,071226
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3298
Polymers90,1432
Non-polymers1,1866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)141.188, 141.188, 42.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 45071.641 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3RN / 2-(hydroxymethyl)cyclopent-2-en-1-one


Mass: 112.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M MgCl2, 0.1M HEPES, 35-40% PEG400, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 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: 1.8→45 Å / Num. all: 30521 / Num. obs: 29638 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 4.2 %
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 18 / Num. unique all: 29638 / Rsym value: 0.58 / % possible all: 98

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Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.2_863)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA

1oya


Resolution: 1.999→44.648 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 2959 10 %random
Rwork0.1824 ---
obs0.1859 29586 99.18 %-
all-30521 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.704 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3266 Å2-0 Å20 Å2
2---1.3266 Å20 Å2
3---2.6531 Å2
Refinement stepCycle: LAST / Resolution: 1.999→44.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 40 226 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083330
X-RAY DIFFRACTIONf_angle_d1.0624524
X-RAY DIFFRACTIONf_dihedral_angle_d14.7161232
X-RAY DIFFRACTIONf_chiral_restr0.076467
X-RAY DIFFRACTIONf_plane_restr0.009592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.03150.26241380.21851246X-RAY DIFFRACTION98
2.0315-2.06650.3241370.22361228X-RAY DIFFRACTION99
2.0665-2.10410.23491370.20771234X-RAY DIFFRACTION99
2.1041-2.14460.24451390.2031255X-RAY DIFFRACTION100
2.1446-2.18830.2571370.19891229X-RAY DIFFRACTION99
2.1883-2.23590.25521390.19721250X-RAY DIFFRACTION98
2.2359-2.28790.25131370.19321237X-RAY DIFFRACTION99
2.2879-2.34510.24341390.18911248X-RAY DIFFRACTION99
2.3451-2.40850.26361380.18731244X-RAY DIFFRACTION99
2.4085-2.47940.21561380.18061234X-RAY DIFFRACTION98
2.4794-2.55940.22571370.1781242X-RAY DIFFRACTION99
2.5594-2.65090.23591420.18111270X-RAY DIFFRACTION99
2.6509-2.7570.22811390.17321255X-RAY DIFFRACTION100
2.757-2.88250.22421420.17981284X-RAY DIFFRACTION100
2.8825-3.03440.20371420.17761268X-RAY DIFFRACTION100
3.0344-3.22450.20651410.18461278X-RAY DIFFRACTION100
3.2245-3.47330.19261430.1751283X-RAY DIFFRACTION100
3.4733-3.82270.20361450.16071302X-RAY DIFFRACTION100
3.8227-4.37550.20451440.1611302X-RAY DIFFRACTION100
4.3755-5.5110.18741480.17421328X-RAY DIFFRACTION99
5.511-44.65870.21211570.21481410X-RAY DIFFRACTION99

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