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- PDB-4gwe: W116L-OYE1 complexed with (R)-carvone -

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Basic information

Entry
Database: PDB / ID: 4gwe
TitleW116L-OYE1 complexed with (R)-carvone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / reductase / enantioselectivity / flipped binding / carvone / enoate reductase / OYE / old yellow enzyme / biocatalysis / atomic resolution / TIM barrel / alpha/beta barrel
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
Chem-07V / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPompeu, 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 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)46,21210
Polymers44,9991
Non-polymers1,2139
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.780, 140.780, 42.760
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-781-

HOH

31A-798-

HOH

41A-903-

HOH

51A-969-

HOH

61A-979-

HOH

71A-1011-

HOH

81A-1039-

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: 44998.590 Da / Num. of mol.: 1 / Mutation: W116L
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) gold / References: UniProt: Q02899, NADPH dehydrogenase

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Non-polymers , 7 types, 599 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M hepes, 0.2M MgCl2, 35%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: X26C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 26, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 70049 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 12.8 % / Biso Wilson estimate: 11.32 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 71
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 10 / Num. unique all: 2020 / % possible all: 52.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA

1oya


Resolution: 1.45→28.156 Å / SU ML: 0.09 / σ(F): 1.34 / Phase error: 12.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1449 7038 10.05 %random
Rwork0.1148 ---
obs0.1178 70001 90.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→28.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 65 590 3817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083413
X-RAY DIFFRACTIONf_angle_d1.2514646
X-RAY DIFFRACTIONf_dihedral_angle_d14.6831289
X-RAY DIFFRACTIONf_chiral_restr0.079479
X-RAY DIFFRACTIONf_plane_restr0.007609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46280.14811280.08181193X-RAY DIFFRACTION52
1.4628-1.480.1421430.08441289X-RAY DIFFRACTION57
1.48-1.49810.14751620.08531409X-RAY DIFFRACTION62
1.4981-1.5170.13951840.08131600X-RAY DIFFRACTION70
1.517-1.5370.1392140.08271921X-RAY DIFFRACTION84
1.537-1.55810.15172340.07962056X-RAY DIFFRACTION91
1.5581-1.58030.13342300.08612063X-RAY DIFFRACTION89
1.5803-1.60390.13782300.08392058X-RAY DIFFRACTION91
1.6039-1.6290.15082380.08552125X-RAY DIFFRACTION93
1.629-1.65570.15512370.08232101X-RAY DIFFRACTION92
1.6557-1.68420.14712450.08852130X-RAY DIFFRACTION94
1.6842-1.71480.13052510.08862183X-RAY DIFFRACTION95
1.7148-1.74780.12812350.08842153X-RAY DIFFRACTION95
1.7478-1.78350.14112470.09652182X-RAY DIFFRACTION95
1.7835-1.82220.14932460.09662199X-RAY DIFFRACTION97
1.8222-1.86460.13742470.09912216X-RAY DIFFRACTION96
1.8646-1.91120.14912480.10252222X-RAY DIFFRACTION97
1.9112-1.96290.13122470.1072230X-RAY DIFFRACTION97
1.9629-2.02070.13052440.10622217X-RAY DIFFRACTION97
2.0207-2.08590.14382490.10332265X-RAY DIFFRACTION98
2.0859-2.16040.12812500.10592234X-RAY DIFFRACTION96
2.1604-2.24680.13522550.1032244X-RAY DIFFRACTION97
2.2468-2.34910.13682540.10762291X-RAY DIFFRACTION99
2.3491-2.47280.14332550.112277X-RAY DIFFRACTION98
2.4728-2.62770.14092540.11582288X-RAY DIFFRACTION98
2.6277-2.83040.13742510.11932307X-RAY DIFFRACTION98
2.8304-3.11490.1562590.13132308X-RAY DIFFRACTION98
3.1149-3.56480.15812600.14212351X-RAY DIFFRACTION99
3.5648-4.48840.1372640.12532370X-RAY DIFFRACTION99
4.4884-28.16130.17672770.16642481X-RAY DIFFRACTION97

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