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- PDB-4gxm: OYE1-W116L in complex with aromatic product of R-carvone dismutation -

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Basic information

Entry
Database: PDB / ID: 4gxm
TitleOYE1-W116L in complex with aromatic product of R-carvone dismutation
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / enoate reductase / OYE / carvone / enanatiocomplementarity / TIM barrel / FMN binding domain / NAD(P)H oxidoreductase / FMN 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
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: 1.362 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
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 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_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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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_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)47,00616
Polymers44,9991
Non-polymers2,00715
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.120, 141.120, 42.920
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-415-

MG

21A-867-

HOH

31A-869-

HOH

41A-884-

HOH

51A-944-

HOH

61A-1112-

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: 44998.590 Da / Num. of mol.: 1 / Mutation: w116L
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, 648 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#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-0WV / 2-methyl-5-(prop-1-en-2-yl)phenol


Mass: 148.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M MgCl2, 0.1M Hepes, 35%PEG400, 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: X26C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 26, 2012
RadiationMonochromator: si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 87102 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 16.5 % / Biso Wilson estimate: 13.08 Å2 / Rsym value: 0.062 / Net I/σ(I): 60.1
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.68 / Num. unique all: 2611 / Rsym value: 0.394 / % possible all: 56.4

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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: 4gbu

4gbu


Resolution: 1.362→34.227 Å / SU ML: 0.08 / Cross valid method: 10% throughout / σ(F): 1.36 / Phase error: 11.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 8695 9.99 %random
Rwork0.1079 ---
obs0.1108 87025 93.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.362→34.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 100 633 3905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013478
X-RAY DIFFRACTIONf_angle_d1.4424725
X-RAY DIFFRACTIONf_dihedral_angle_d17.5971332
X-RAY DIFFRACTIONf_chiral_restr0.112482
X-RAY DIFFRACTIONf_plane_restr0.009619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3622-1.37760.17991880.12261693X-RAY DIFFRACTION61
1.3776-1.39380.17021990.10981786X-RAY DIFFRACTION66
1.3938-1.41080.14912090.0971915X-RAY DIFFRACTION70
1.4108-1.42870.1552230.09682008X-RAY DIFFRACTION72
1.4287-1.44750.14432370.09462146X-RAY DIFFRACTION78
1.4475-1.46730.1322510.09282249X-RAY DIFFRACTION82
1.4673-1.48830.12982680.09172442X-RAY DIFFRACTION88
1.4883-1.51050.1382890.09122598X-RAY DIFFRACTION96
1.5105-1.53410.14023050.08632752X-RAY DIFFRACTION99
1.5341-1.55930.12823020.08052726X-RAY DIFFRACTION100
1.5593-1.58610.12833110.07832795X-RAY DIFFRACTION100
1.5861-1.6150.12493000.0782706X-RAY DIFFRACTION100
1.615-1.6460.1213090.08082779X-RAY DIFFRACTION100
1.646-1.67960.11753040.08112738X-RAY DIFFRACTION100
1.6796-1.71620.11743080.0842766X-RAY DIFFRACTION100
1.7162-1.75610.1193060.0892751X-RAY DIFFRACTION100
1.7561-1.80.13693110.09182800X-RAY DIFFRACTION100
1.8-1.84870.11983040.09422742X-RAY DIFFRACTION100
1.8487-1.90310.13263090.0992784X-RAY DIFFRACTION100
1.9031-1.96450.13913100.10182793X-RAY DIFFRACTION100
1.9645-2.03470.12383070.09872762X-RAY DIFFRACTION100
2.0347-2.11610.12423110.09652791X-RAY DIFFRACTION100
2.1161-2.21240.11913090.09492781X-RAY DIFFRACTION100
2.2124-2.32910.13013100.09562802X-RAY DIFFRACTION100
2.3291-2.47490.13163130.10192801X-RAY DIFFRACTION100
2.4749-2.6660.13323140.10882830X-RAY DIFFRACTION100
2.666-2.93410.12833130.122829X-RAY DIFFRACTION100
2.9341-3.35840.15353180.12592852X-RAY DIFFRACTION100
3.3584-4.230.13963210.11742898X-RAY DIFFRACTION100
4.23-34.23740.16923360.16133015X-RAY DIFFRACTION99

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