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- PDB-4k7v: OYE1-W116A complexed with (R)-carvone -

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Basic information

Entry
Database: PDB / ID: 4k7v
TitleOYE1-W116A complexed with (R)-carvone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / carvone / TIM barrel / NADPH dehydrogenase 1
Function / homology
Function and homology information


NADPH dehydrogenase / pentaerythritol trinitrate reductase activity / 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: 1.516 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 17, 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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_label_seq_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)45,9078
Polymers44,9571
Non-polymers9517
Water9,008500
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,81416
Polymers89,9132
Non-polymers1,90114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)140.853, 140.853, 42.841
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-873-

HOH

31A-939-

HOH

41A-956-

HOH

51A-977-

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: 44956.508 Da / Num. of mol.: 1 / Mutation: W116A
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 , 7 types, 507 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 47.95 %
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: 1.516→35.425 Å / Num. obs: 66347 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 38.2
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.25 / Num. unique all: 6583 / % possible all: 99.5

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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: 1.516→35.425 Å / SU ML: 0.13 / σ(F): 1.33 / Phase error: 17.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.183 6154 10.02 %Random 10%
Rwork0.1447 ---
obs0.1486 66347 98 %-
all-65970 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.516→35.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 62 500 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083350
X-RAY DIFFRACTIONf_angle_d1.2424547
X-RAY DIFFRACTIONf_dihedral_angle_d13.7061251
X-RAY DIFFRACTIONf_chiral_restr0.076470
X-RAY DIFFRACTIONf_plane_restr0.006594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.516-1.53320.26382130.17531909X-RAY DIFFRACTION95
1.5332-1.55120.23212160.15221956X-RAY DIFFRACTION100
1.5512-1.57010.21432210.13481977X-RAY DIFFRACTION99
1.5701-1.590.19932190.12541977X-RAY DIFFRACTION99
1.59-1.61090.21112150.12191945X-RAY DIFFRACTION99
1.6109-1.6330.19322230.12092004X-RAY DIFFRACTION99
1.633-1.65630.21022200.11991974X-RAY DIFFRACTION98
1.6563-1.6810.21292150.12341937X-RAY DIFFRACTION99
1.681-1.70730.18832190.11431966X-RAY DIFFRACTION99
1.7073-1.73530.20022190.11281968X-RAY DIFFRACTION98
1.7353-1.76520.17392160.11011947X-RAY DIFFRACTION98
1.7652-1.79730.19142180.11611972X-RAY DIFFRACTION98
1.7973-1.83190.20342180.12951957X-RAY DIFFRACTION98
1.8319-1.86930.19392200.15161974X-RAY DIFFRACTION98
1.8693-1.90990.28312050.21591799X-RAY DIFFRACTION91
1.9099-1.95440.35972080.28321837X-RAY DIFFRACTION91
1.9544-2.00320.18282180.14291955X-RAY DIFFRACTION99
2.0032-2.05740.17952230.13051995X-RAY DIFFRACTION99
2.0574-2.11790.18572210.13081993X-RAY DIFFRACTION99
2.1179-2.18630.14782220.12681999X-RAY DIFFRACTION100
2.1863-2.26440.26562130.18491923X-RAY DIFFRACTION94
2.2644-2.3550.15992190.12271968X-RAY DIFFRACTION98
2.355-2.46220.14962250.11172030X-RAY DIFFRACTION100
2.4622-2.5920.14762230.11632011X-RAY DIFFRACTION100
2.592-2.75430.13812270.11662037X-RAY DIFFRACTION100
2.7543-2.96690.14852270.13632046X-RAY DIFFRACTION100
2.9669-3.26520.17412300.14982067X-RAY DIFFRACTION100
3.2652-3.73730.17512290.15252063X-RAY DIFFRACTION100
3.7373-4.70690.16222220.13691996X-RAY DIFFRACTION95
4.7069-35.43420.18212430.17652181X-RAY DIFFRACTION98

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