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- PDB-4k8e: OYE1-W116V complexed with the aromatic product of (R)-carvone dis... -

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Basic information

Entry
Database: PDB / ID: 4k8e
TitleOYE1-W116V complexed with the aromatic product of (R)-carvone dismutation
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / carvone / TIM-barrel / NADPH dehydrogenase 1
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-methyl-5-(prop-1-en-2-yl)phenol / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.269 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
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)46,50716
Polymers44,9851
Non-polymers1,52315
Water11,566642
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,01532
Polymers89,9692
Non-polymers3,04630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)141.135, 141.135, 42.850
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-402-

MG

21A-778-

HOH

31A-1001-

HOH

41A-1053-

HOH

51A-1065-

HOH

61A-1129-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 44984.562 Da / Num. of mol.: 1 / Mutation: W116V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q02899, NADPH dehydrogenase

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Non-polymers , 8 types, 657 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-0WV / 2-methyl-5-(prop-1-en-2-yl)phenol


Mass: 148.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 48.14 %
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: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 15, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.269→24.2088 Å / Num. obs: 113545 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.59
Reflection shellResolution: 1.27→1.32 Å / Redundancy: 9 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.47 / Num. unique all: 11082 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.269→24.204 Å / SU ML: 0.1 / σ(F): 1.37 / Phase error: 9.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1267 11028 10 %10% random
Rwork0.1066 ---
obs0.1086 113482 99.44 %-
all-113545 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.269→24.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 97 642 3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073531
X-RAY DIFFRACTIONf_angle_d1.2944808
X-RAY DIFFRACTIONf_dihedral_angle_d14.3891375
X-RAY DIFFRACTIONf_chiral_restr0.08493
X-RAY DIFFRACTIONf_plane_restr0.008630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2694-1.28390.19523690.19013322X-RAY DIFFRACTION99
1.2839-1.2990.19193650.16053293X-RAY DIFFRACTION97
1.299-1.31480.17783720.1433345X-RAY DIFFRACTION100
1.3148-1.33150.1783720.13163352X-RAY DIFFRACTION99
1.3315-1.3490.14593670.11643304X-RAY DIFFRACTION98
1.349-1.36740.14683750.10633376X-RAY DIFFRACTION100
1.3674-1.3870.1493710.10223337X-RAY DIFFRACTION98
1.387-1.40770.13023730.10023357X-RAY DIFFRACTION100
1.4077-1.42970.13683730.10013355X-RAY DIFFRACTION98
1.4297-1.45310.1323710.09893337X-RAY DIFFRACTION100
1.4531-1.47820.12943770.09723390X-RAY DIFFRACTION99
1.4782-1.5050.11893720.0913360X-RAY DIFFRACTION100
1.505-1.5340.10623770.07773385X-RAY DIFFRACTION99
1.534-1.56530.10583750.07293372X-RAY DIFFRACTION100
1.5653-1.59930.10113740.07233370X-RAY DIFFRACTION99
1.5993-1.63650.10283800.0733419X-RAY DIFFRACTION100
1.6365-1.67740.11253750.07163385X-RAY DIFFRACTION100
1.6774-1.72280.10033800.07513410X-RAY DIFFRACTION100
1.7228-1.77350.1033770.07583404X-RAY DIFFRACTION100
1.7735-1.83070.11263780.07993398X-RAY DIFFRACTION100
1.8307-1.89610.11433790.0823407X-RAY DIFFRACTION100
1.8961-1.9720.11143810.08923435X-RAY DIFFRACTION100
1.972-2.06170.11113830.093441X-RAY DIFFRACTION100
2.0617-2.17030.11673840.09243459X-RAY DIFFRACTION100
2.1703-2.30620.11733820.09553430X-RAY DIFFRACTION100
2.3062-2.48410.1123840.10083458X-RAY DIFFRACTION100
2.4841-2.73370.12483860.10683485X-RAY DIFFRACTION100
2.7337-3.12860.12263910.12083510X-RAY DIFFRACTION100
3.1286-3.9390.13473930.12533541X-RAY DIFFRACTION100
3.939-24.20880.16234120.15833697X-RAY DIFFRACTION99

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