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- PDB-4k7y: Oye1-w116t -

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Basic information

Entry
Database: PDB / ID: 4k7y
TitleOye1-w116t
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
FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 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)45,92811
Polymers44,9871
Non-polymers94210
Water11,998666
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,85622
Polymers89,9732
Non-polymers1,88320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)141.327, 141.327, 42.832
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-409-

MG

21A-770-

HOH

31A-771-

HOH

41A-957-

HOH

51A-993-

HOH

61A-1107-

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: 44986.535 Da / Num. of mol.: 1 / Mutation: W116T
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 , 6 types, 676 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
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: 1.199→23.5961 Å / Num. obs: 135203 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.21
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.9 / Num. unique all: 13338 / % possible all: 100

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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: 1.199→23.592 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 9.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1352 12978 10 %random 10%
Rwork0.1154 ---
obs0.1174 135136 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.199→23.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 58 666 3895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073535
X-RAY DIFFRACTIONf_angle_d1.3644828
X-RAY DIFFRACTIONf_dihedral_angle_d14.2321372
X-RAY DIFFRACTIONf_chiral_restr0.081499
X-RAY DIFFRACTIONf_plane_restr0.008637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1991-1.21270.30674210.28123795X-RAY DIFFRACTION95
1.2127-1.2270.27694510.24014051X-RAY DIFFRACTION100
1.227-1.2420.22164420.21273975X-RAY DIFFRACTION100
1.242-1.25770.19244470.17394024X-RAY DIFFRACTION100
1.2577-1.27420.20084430.1563989X-RAY DIFFRACTION100
1.2742-1.29170.17154500.14264054X-RAY DIFFRACTION100
1.2917-1.31010.15364440.12554000X-RAY DIFFRACTION100
1.3101-1.32970.15254460.12084003X-RAY DIFFRACTION100
1.3297-1.35050.14694480.10874030X-RAY DIFFRACTION100
1.3505-1.37260.13464450.10494012X-RAY DIFFRACTION100
1.3726-1.39630.14034470.11234030X-RAY DIFFRACTION100
1.3963-1.42170.13154480.10624020X-RAY DIFFRACTION100
1.4217-1.4490.13454500.10714052X-RAY DIFFRACTION100
1.449-1.47860.13814480.1114035X-RAY DIFFRACTION100
1.4786-1.51070.12734450.10614009X-RAY DIFFRACTION100
1.5107-1.54590.13154490.1044039X-RAY DIFFRACTION100
1.5459-1.58450.10614530.07614081X-RAY DIFFRACTION100
1.5845-1.62730.10974450.0773999X-RAY DIFFRACTION100
1.6273-1.67520.10054510.07524056X-RAY DIFFRACTION100
1.6752-1.72930.10474500.07984054X-RAY DIFFRACTION100
1.7293-1.79110.11524520.08314073X-RAY DIFFRACTION100
1.7911-1.86270.10854530.08594073X-RAY DIFFRACTION100
1.8627-1.94750.11364530.09194079X-RAY DIFFRACTION100
1.9475-2.05010.11274530.09324075X-RAY DIFFRACTION100
2.0501-2.17850.11274530.0934077X-RAY DIFFRACTION100
2.1785-2.34650.10944550.09974098X-RAY DIFFRACTION100
2.3465-2.58240.12614590.11164129X-RAY DIFFRACTION100
2.5824-2.95550.13684620.12294152X-RAY DIFFRACTION100
2.9555-3.72120.14924650.1314185X-RAY DIFFRACTION100
3.7212-23.59610.15534860.15294373X-RAY DIFFRACTION99

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