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- PDB-1oyc: OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, L... -

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Basic information

Entry
Database: PDB / ID: 1oyc
TitleOLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, LIGAND BINDING AND COMPARISON WITH RELATED FLAVOPROTEINS
ComponentsOLD YELLOW ENZYMENADPH dehydrogenase
KeywordsOXIDOREDUCTASE(FLAVOPROTEIN)
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 / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFox, K.M. / Karplus, P.A.
CitationJournal: Structure / Year: 1994
Title: Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins.
Authors: Fox, K.M. / Karplus, P.A.
History
DepositionAug 25, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: OLD YELLOW ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5282
Polymers45,0721
Non-polymers4561
Water2,270126
1
A: OLD YELLOW ENZYME
hetero molecules

A: OLD YELLOW ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0564
Polymers90,1432
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)142.880, 142.880, 43.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 44

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Components

#1: Protein OLD YELLOW ENZYME / NADPH dehydrogenase


Mass: 45071.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: PET / Strain (production host): PET / References: UniProt: Q02899, NADPH dehydrogenase
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Fox, K.M., (1993) J. Mol. Biol., 234, 502.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mM1dropNaCl
40.01 Mphrnylmethylsulfonyl fluoride1drop
50.1 MHEPES1reservoir
635 %(w/v)PEG4001reservoir
70.2 M1reservoirMgCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 26517 / % possible obs: 71.6 %
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 63008 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 2 Å
RfactorNum. reflection
Rfree0.259 -
Rwork0.17 -
obs0.17 63008
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 35 378 4302
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rwork: 0.17 / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_deg3.3

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