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- PDB-3rnd: W116I-OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone -

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Basic information

Entry
Database: PDB / ID: 3rnd
TitleW116I-OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / TIM Barrel / NADPH
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
2-(hydroxymethyl)cyclopent-2-en-1-one / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: ACS Catalysis / Year: 2011
Title: Biocatalytic Reductions of Baylis-Hillman Adducts
Authors: Walton, A.Z. / Conerly, W.C. / Pompeu, Y.A. / Sullivan, B.T. / Stewart, J.D.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Derived calculations
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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)45,4845
Polymers44,8671
Non-polymers6174
Water7,170398
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,96910
Polymers89,7352
Non-polymers1,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)141.180, 141.180, 42.789
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-403-

MG

21A-405-

HOH

31A-748-

HOH

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Components

#1: Protein NADPH dehydrogenase 1 / Old yellow enzyme 1


Mass: 44867.395 Da / Num. of mol.: 1 / Mutation: W116I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET-3b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q02899, NADPH dehydrogenase
#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-3RN / 2-(hydroxymethyl)cyclopent-2-en-1-one


Mass: 112.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 48.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.1M hepes, 35% PEG 400, 0.2M Mg2Cl2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 585768 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYA

1oya


Resolution: 1.4→44.645 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 8432 10 %random
Rwork0.15 ---
all0.1519 85421 --
obs0.151 84304 98.7 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 41 398 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073379
X-RAY DIFFRACTIONf_angle_d1.1364599
X-RAY DIFFRACTIONf_dihedral_angle_d13.631261
X-RAY DIFFRACTIONf_chiral_restr0.08474
X-RAY DIFFRACTIONf_plane_restr0.013603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.4160.21962590.19632368X-RAY DIFFRACTION93
1.416-1.43260.20622690.17342390X-RAY DIFFRACTION95
1.4326-1.45010.19512720.16242415X-RAY DIFFRACTION96
1.4501-1.46850.19392710.16212438X-RAY DIFFRACTION96
1.4685-1.48780.17732750.14272464X-RAY DIFFRACTION98
1.4878-1.50820.18452760.13692453X-RAY DIFFRACTION98
1.5082-1.52970.18132760.13172477X-RAY DIFFRACTION97
1.5297-1.55250.17032750.12622472X-RAY DIFFRACTION98
1.5525-1.57680.17532750.12352480X-RAY DIFFRACTION98
1.5768-1.60270.15842770.11052496X-RAY DIFFRACTION99
1.6027-1.63030.15632740.11442496X-RAY DIFFRACTION99
1.6303-1.65990.14922820.10972537X-RAY DIFFRACTION99
1.6599-1.69190.15412780.11342492X-RAY DIFFRACTION99
1.6919-1.72640.15042780.10722513X-RAY DIFFRACTION99
1.7264-1.76390.14912810.10832547X-RAY DIFFRACTION99
1.7639-1.8050.13962810.11582537X-RAY DIFFRACTION100
1.805-1.85010.1672810.12052532X-RAY DIFFRACTION100
1.8501-1.90010.14032820.12172537X-RAY DIFFRACTION100
1.9001-1.95610.15322830.12892553X-RAY DIFFRACTION100
1.9561-2.01920.15522850.13592563X-RAY DIFFRACTION100
2.0192-2.09140.16922820.13912529X-RAY DIFFRACTION100
2.0914-2.17510.15662870.14162580X-RAY DIFFRACTION100
2.1751-2.27410.15912850.14412567X-RAY DIFFRACTION100
2.2741-2.3940.16092850.1442577X-RAY DIFFRACTION100
2.394-2.54390.17012870.15212585X-RAY DIFFRACTION100
2.5439-2.74030.18622870.15852577X-RAY DIFFRACTION100
2.7403-3.01610.16592910.16852614X-RAY DIFFRACTION100
3.0161-3.45230.16542900.17512613X-RAY DIFFRACTION100
3.4523-4.3490.15912960.15452666X-RAY DIFFRACTION100
4.349-44.66770.20413120.18712804X-RAY DIFFRACTION100

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