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- PDB-4qai: P. stipitis OYE2.6-Y78W -

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Basic information

Entry
Database: PDB / ID: 4qai
TitleP. stipitis OYE2.6-Y78W
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / TIM barrel / flavin oxidoreductase / alkene reductase
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
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
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSullivan, B. / Walton, A.Z. / Stewart, J.D.
CitationJournal: ACS CATALYSIS / Year: 2014
Title: Residues Controlling Facial Selectivity in an Alkene Reductase and Semirational Alterations to Create Stereocomplementary Variants.
Authors: Walton, A.Z. / Sullivan, B. / Patterson-Orazem, A.C. / Stewart, J.D.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH dehydrogenase
B: NADPH dehydrogenase
C: NADPH dehydrogenase
D: NADPH dehydrogenase
E: NADPH dehydrogenase
F: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,65012
Polymers271,9116
Non-polymers2,7386
Water39622
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5504
Polymers90,6372
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
2
B: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5504
Polymers90,6372
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
3
C: NADPH dehydrogenase
E: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5504
Polymers90,6372
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADPH dehydrogenase
F: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5504
Polymers90,6372
Non-polymers9132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)226.787, 226.787, 360.851
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
NADPH dehydrogenase /


Mass: 45318.578 Da / Num. of mol.: 6 / Mutation: Y78W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (fungus) / Strain: CBS 6054 / Gene: OYE 2.6, OYE2.6, PICST_44614 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-gold (DE3) / References: UniProt: A3LT82
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3M sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.541 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.75→48.65 Å / Num. all: 92137 / Num. obs: 92137 / % possible obs: 99.47 %

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Processing

Software
NameClassification
CBASSdata collection
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OYE 2.6 Y78W, I113C

Resolution: 2.75→48.65 Å
RfactorNum. reflectionSelection details
Rfree0.28 -0.1
Rwork0.224 --
all-92137 -
obs-92137 -
Refinement stepCycle: LAST / Resolution: 2.75→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19056 0 186 22 19264

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