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- PDB-3upw: Pichia Stipitis OYE2.6 complexed with nicotinamide -

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Basic information

Entry
Database: PDB / ID: 3upw
TitlePichia Stipitis OYE2.6 complexed with nicotinamide
ComponentsOld Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
KeywordsOXIDOREDUCTASE / OYE / old yellow enzyme / FMN / Alkene Reductase / assymetric alkene reduction / OYE1 homologue / TIM Barrel / NADPH Oxidoreductase / NAD(P)H
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
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 / MALONIC ACID / NICOTINAMIDE / NADPH dehydrogenase
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: Adv.Synth.Catal. / Year: 2012
Title: Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions
Authors: Pompeu, Y.A. / Sullivan, B. / Walton, A.Z. / Stewart, J.D.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,27810
Polymers45,2961
Non-polymers9839
Water8,017445
1
A: Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
hetero molecules

A: Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,55620
Polymers90,5912
Non-polymers1,96518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5910 Å2
ΔGint-106 kcal/mol
Surface area29580 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)127.306, 127.306, 123.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-526-

HOH

31A-652-

HOH

41A-656-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase


Mass: 45295.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (fungus) / Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: OYE2.6, PICST_44614 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A3LT82, NADPH dehydrogenase

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Non-polymers , 5 types, 454 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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Na Malonate, 2%iPrOH, pH 7, 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: Aug 15, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 54454 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 10.7 % / Biso Wilson estimate: 22.44 Å2 / Rsym value: 0.047 / Net I/σ(I): 37.1
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1786 / Rsym value: 0.55 / % possible all: 96

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OYA
Resolution: 1.781→44.241 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 5649 10 %10% random
Rwork0.1577 ---
obs0.1605 54454 99.76 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.738 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7835 Å20 Å20 Å2
2---0.7835 Å20 Å2
3---1.567 Å2
Refinement stepCycle: LAST / Resolution: 1.781→44.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 65 445 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073350
X-RAY DIFFRACTIONf_angle_d1.0494567
X-RAY DIFFRACTIONf_dihedral_angle_d15.0531236
X-RAY DIFFRACTIONf_chiral_restr0.074504
X-RAY DIFFRACTIONf_plane_restr0.004595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7809-1.80120.30321780.28621608X-RAY DIFFRACTION96
1.8012-1.82240.3081840.25041650X-RAY DIFFRACTION98
1.8224-1.84460.27341850.23281665X-RAY DIFFRACTION100
1.8446-1.86790.2331840.19951658X-RAY DIFFRACTION100
1.8679-1.89250.21761850.1911658X-RAY DIFFRACTION100
1.8925-1.91840.2381840.1921662X-RAY DIFFRACTION100
1.9184-1.94580.21841870.18151685X-RAY DIFFRACTION100
1.9458-1.97490.22171840.16921653X-RAY DIFFRACTION100
1.9749-2.00570.20591880.16241689X-RAY DIFFRACTION100
2.0057-2.03860.21211870.15721677X-RAY DIFFRACTION100
2.0386-2.07380.19931830.16331665X-RAY DIFFRACTION100
2.0738-2.11150.18821880.16411680X-RAY DIFFRACTION100
2.1115-2.15210.18041860.15871675X-RAY DIFFRACTION100
2.1521-2.1960.17331880.14841692X-RAY DIFFRACTION100
2.196-2.24380.18221860.14851680X-RAY DIFFRACTION100
2.2438-2.2960.18841880.15781685X-RAY DIFFRACTION100
2.296-2.35340.19391870.15541680X-RAY DIFFRACTION100
2.3534-2.4170.16121860.15181687X-RAY DIFFRACTION100
2.417-2.48810.18371880.15471686X-RAY DIFFRACTION100
2.4881-2.56840.18661900.16061706X-RAY DIFFRACTION100
2.5684-2.66020.18521870.16911689X-RAY DIFFRACTION100
2.6602-2.76670.2091900.18281703X-RAY DIFFRACTION100
2.7667-2.89260.20681890.17471702X-RAY DIFFRACTION100
2.8926-3.04510.20041900.17121710X-RAY DIFFRACTION100
3.0451-3.23580.18861900.15891714X-RAY DIFFRACTION100
3.2358-3.48560.17221900.14331712X-RAY DIFFRACTION100
3.4856-3.83610.16921940.13121739X-RAY DIFFRACTION100
3.8361-4.39080.15081950.11351753X-RAY DIFFRACTION100
4.3908-5.53030.13141980.13081781X-RAY DIFFRACTION100
5.5303-44.25420.19922100.17921891X-RAY DIFFRACTION100

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