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- PDB-4ge8: OYE1-W116I complexed with (s)-Carvone -

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Basic information

Entry
Database: PDB / ID: 4ge8
TitleOYE1-W116I complexed with (s)-Carvone
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / CARVONE / ENOATE REDUCTASE / ALKENE REDUCTASE / ENENATIOSELECTIVITY / SUBSTRATE FLIPPING / tim barrel / nad(p)h
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
Chem-0WU / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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
DepositionAug 1, 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: 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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)46,78115
Polymers44,9991
Non-polymers1,78214
Water8,377465
1
A: NADPH dehydrogenase 1
hetero molecules

A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,56230
Polymers89,9972
Non-polymers3,56528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)140.928, 140.928, 42.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 44998.590 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) gold / References: UniProt: Q02899, NADPH dehydrogenase

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Non-polymers , 7 types, 479 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Chemical ChemComp-0WU / (5S)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one / S-carvone


Mass: 150.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M MgCl2, 35%peg400, 0.1M NaHepes, 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 5, 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: 1.45→28.6 Å / Num. obs: 68916 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11.1 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.78 / Num. unique all: 6767 / % possible all: 98

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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: 1OYA

1oya


Resolution: 1.499→24.169 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 6891 10 %random
Rwork0.1365 ---
obs0.1399 68913 99.75 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→24.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 91 465 3725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083439
X-RAY DIFFRACTIONf_angle_d1.2014669
X-RAY DIFFRACTIONf_dihedral_angle_d15.2211317
X-RAY DIFFRACTIONf_chiral_restr0.078480
X-RAY DIFFRACTIONf_plane_restr0.006610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.51590.28462250.21252026X-RAY DIFFRACTION98
1.5159-1.53370.21092250.18152022X-RAY DIFFRACTION100
1.5337-1.55240.20562260.15352033X-RAY DIFFRACTION100
1.5524-1.57210.21312250.15262024X-RAY DIFFRACTION100
1.5721-1.59280.22432250.14682034X-RAY DIFFRACTION100
1.5928-1.61460.18712290.14262052X-RAY DIFFRACTION100
1.6146-1.63760.21342270.13932045X-RAY DIFFRACTION100
1.6376-1.66210.20222240.13982013X-RAY DIFFRACTION100
1.6621-1.6880.18042280.13372058X-RAY DIFFRACTION100
1.688-1.71570.19822260.12172035X-RAY DIFFRACTION100
1.7157-1.74530.17092270.12182043X-RAY DIFFRACTION100
1.7453-1.7770.1872300.12532073X-RAY DIFFRACTION100
1.777-1.81120.17242250.1192028X-RAY DIFFRACTION100
1.8112-1.84810.16892320.11862081X-RAY DIFFRACTION100
1.8481-1.88830.16622250.1132033X-RAY DIFFRACTION100
1.8883-1.93220.17672320.11922075X-RAY DIFFRACTION100
1.9322-1.98050.14662270.11752041X-RAY DIFFRACTION100
1.9805-2.0340.14532300.10992077X-RAY DIFFRACTION100
2.034-2.09390.1552270.11342042X-RAY DIFFRACTION100
2.0939-2.16140.16552300.11542075X-RAY DIFFRACTION100
2.1614-2.23860.1522340.11892102X-RAY DIFFRACTION100
2.2386-2.32820.17312270.11532040X-RAY DIFFRACTION100
2.3282-2.4340.16472300.12382072X-RAY DIFFRACTION100
2.434-2.56220.17232320.12632082X-RAY DIFFRACTION100
2.5622-2.72250.17082330.12632103X-RAY DIFFRACTION100
2.7225-2.93240.17232330.13282090X-RAY DIFFRACTION100
2.9324-3.22690.17382370.14262132X-RAY DIFFRACTION100
3.2269-3.69240.15522340.14032114X-RAY DIFFRACTION100
3.6924-4.64660.15372400.1312157X-RAY DIFFRACTION100
4.6466-24.17210.1842460.19632220X-RAY DIFFRACTION97

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