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- PDB-4gbu: OYE1-W116A in complex with aromatic product of S-carvone dismutation -

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Basic information

Entry
Database: PDB / ID: 4gbu
TitleOYE1-W116A in complex with aromatic product of S-carvone dismutation
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / alpha/beta barrel / enenone reductase / alkene reductase / NADPH oxidoreductase / carvone / enenatioselectivity / binding mode / dismutation / ligand / TIM barrel / NAD(P)H oxidoreductase / NAD(P)H
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
2-methyl-5-(prop-1-en-2-yl)phenol / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.179 Å
AuthorsPompeu, 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
DepositionJul 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_sheet / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_sheet.number_strands / _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)46,98717
Polymers44,9571
Non-polymers2,03016
Water11,854658
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97434
Polymers89,9132
Non-polymers4,06132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)141.121, 141.121, 42.813
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-407-

MG

21A-1048-

HOH

31A-1089-

HOH

41A-1139-

HOH

51A-1152-

HOH

61A-1154-

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: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q02899, NADPH dehydrogenase

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Non-polymers , 7 types, 674 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0WV / 2-methyl-5-(prop-1-en-2-yl)phenol


Mass: 148.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 47.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 35% Peg400, 0.2M MgCl2, 0.1M Na Hepes, 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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.18→24 Å / Num. obs: 999641 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 25.2
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.04 / Num. unique all: 13937 / Rsym value: 0.554 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RND

3rnd


Resolution: 1.179→21.037 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 9.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.121 14125 10 %random 10%
Rwork0.0999 ---
obs0.102 141257 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.179→21.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 107 658 3932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013472
X-RAY DIFFRACTIONf_angle_d1.4754716
X-RAY DIFFRACTIONf_dihedral_angle_d17.4781341
X-RAY DIFFRACTIONf_chiral_restr0.132482
X-RAY DIFFRACTIONf_plane_restr0.01617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1795-1.19290.20124630.17084168X-RAY DIFFRACTION99
1.1929-1.20690.19434600.15234146X-RAY DIFFRACTION100
1.2069-1.22160.17194700.14214221X-RAY DIFFRACTION100
1.2216-1.23710.16664610.13824144X-RAY DIFFRACTION100
1.2371-1.25340.16744670.13584215X-RAY DIFFRACTION100
1.2534-1.27050.16084690.1374217X-RAY DIFFRACTION100
1.2705-1.28870.15424640.13034170X-RAY DIFFRACTION100
1.2887-1.30790.16124690.11994223X-RAY DIFFRACTION100
1.3079-1.32840.14824680.11014210X-RAY DIFFRACTION100
1.3284-1.35010.13524660.10174204X-RAY DIFFRACTION100
1.3501-1.37340.12784700.09294222X-RAY DIFFRACTION100
1.3734-1.39840.12054670.09074195X-RAY DIFFRACTION100
1.3984-1.42530.12764710.08794243X-RAY DIFFRACTION100
1.4253-1.45440.11994660.08614196X-RAY DIFFRACTION100
1.4544-1.4860.11794700.08874231X-RAY DIFFRACTION100
1.486-1.52050.10784710.07684242X-RAY DIFFRACTION100
1.5205-1.55850.10394660.06624192X-RAY DIFFRACTION100
1.5585-1.60070.09774730.06624257X-RAY DIFFRACTION100
1.6007-1.64780.0914730.06354256X-RAY DIFFRACTION100
1.6478-1.70090.09314710.06764236X-RAY DIFFRACTION100
1.7009-1.76170.09444690.07024228X-RAY DIFFRACTION100
1.7617-1.83220.09894730.07444256X-RAY DIFFRACTION100
1.8322-1.91550.114750.07714268X-RAY DIFFRACTION100
1.9155-2.01640.10754730.08064264X-RAY DIFFRACTION100
2.0164-2.14260.09824750.08354288X-RAY DIFFRACTION100
2.1426-2.30790.10224740.08284260X-RAY DIFFRACTION100
2.3079-2.53980.11174770.0924300X-RAY DIFFRACTION99
2.5398-2.90650.12164770.10644290X-RAY DIFFRACTION99
2.9065-3.65870.12714830.124346X-RAY DIFFRACTION99
3.6587-21.04040.144940.13824444X-RAY DIFFRACTION97

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