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- PDB-7mbf: codeinone reductase isoform 1.3 Apo form -

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Basic information

Entry
Database: PDB / ID: 7mbf
Titlecodeinone reductase isoform 1.3 Apo form
ComponentsNADPH-dependent codeinone reductase 1-3
KeywordsOXIDOREDUCTASE / aldo-keto reductase / opium poppy / Benzylisoquinoline alkaloid / biosynthesis
Function / homology
Function and homology information


codeinone reductase (NADPH) / codeinone reductase (NADPH) activity / D-threo-aldose 1-dehydrogenase activity / alkaloid metabolic process / cytosol
Similarity search - Function
Aldo-keto reductase family 4A/B / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADPH-dependent codeinone reductase 1-3
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCarr, S.C. / Ng, K.K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)05287 Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural studies of codeinone reductase reveal novel insights into aldo-keto reductase function in benzylisoquinoline alkaloid biosynthesis.
Authors: Carr, S.C. / Torres, M.A. / Morris, J.S. / Facchini, P.J. / Ng, K.K.S.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent codeinone reductase 1-3
B: NADPH-dependent codeinone reductase 1-3
C: NADPH-dependent codeinone reductase 1-3
D: NADPH-dependent codeinone reductase 1-3
E: NADPH-dependent codeinone reductase 1-3
F: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)218,0516
Polymers218,0516
Non-polymers00
Water2,954164
1
A: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)36,3421
Polymers36,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)36,3421
Polymers36,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)36,3421
Polymers36,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)36,3421
Polymers36,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)36,3421
Polymers36,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NADPH-dependent codeinone reductase 1-3


Theoretical massNumber of molelcules
Total (without water)36,3421
Polymers36,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.936, 90.937, 144.801
Angle α, β, γ (deg.)90.000, 93.529, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
NADPH-dependent codeinone reductase 1-3


Mass: 36341.902 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: COR1.3 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q9SQ68, codeinone reductase (NADPH)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.39 Å3/Da / Density % sol: 48.7 % / Description: prism
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% polyethylene glycol 3350, 0.35M sodium chloride, 8% glycerol, 2mM DTT, 0.1M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2019
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 68275 / % possible obs: 86.2 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 39.01 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.143 / Rrim(I) all: 0.258 / Rsym value: 0.214 / Net I/av σ(I): 3.88 / Net I/σ(I): 2.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 3743 / CC1/2: 0.523 / CC star: 0.827 / Rpim(I) all: 0.735 / Rrim(I) all: 1.215 / Rsym value: 0.958 / % possible all: 47.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIX1.18.2_3874refinement
HKL-30002.3.12data reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zgd

1zgd


Resolution: 2.4→43.37 Å / SU ML: 0.4144 / Cross valid method: FREE R-VALUE / Phase error: 32.3644
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 2004 2.98 %
Rwork0.2194 65181 -
obs0.2211 67185 84.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14360 0 0 164 14524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002214649
X-RAY DIFFRACTIONf_angle_d0.489819809
X-RAY DIFFRACTIONf_chiral_restr0.03972244
X-RAY DIFFRACTIONf_plane_restr0.0042513
X-RAY DIFFRACTIONf_dihedral_angle_d20.88725436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.3487760.3122222X-RAY DIFFRACTION40.34
2.46-2.530.3652940.31492784X-RAY DIFFRACTION51.11
2.53-2.610.3406970.31623183X-RAY DIFFRACTION58.09
2.61-2.690.37841230.31914004X-RAY DIFFRACTION73.01
2.69-2.790.3491430.31334707X-RAY DIFFRACTION85.69
2.79-2.90.35991650.3065214X-RAY DIFFRACTION94.83
2.9-3.030.37251560.28995329X-RAY DIFFRACTION95.89
3.03-3.190.33191620.25135182X-RAY DIFFRACTION94.48
3.19-3.390.29811700.23185379X-RAY DIFFRACTION98.14
3.39-3.650.26711610.21235484X-RAY DIFFRACTION98.5
3.65-4.020.22351610.18355401X-RAY DIFFRACTION97.73
4.02-4.60.23711750.16315369X-RAY DIFFRACTION96.91
4.6-5.790.24161600.18045471X-RAY DIFFRACTION98.34
5.79-43.370.23031610.18775452X-RAY DIFFRACTION95.83

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