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- PDB-3o26: The structure of salutaridine reductase from Papaver somniferum. -

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Basic information

Entry
Database: PDB / ID: 3o26
TitleThe structure of salutaridine reductase from Papaver somniferum.
ComponentsSalutaridine reductase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductases
Function / homology
Function and homology information


salutaridine reductase (NADPH) / salutaridine reductase (NADPH) activity / morphine biosynthetic process / NADP binding / membrane
Similarity search - Function
Carbonyl reductase [NADPH] 1-like / short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Salutaridine reductase
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.91 Å
AuthorsHigashi, Y. / Kutchen, T.M. / Smith, T.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The atomic structure of salutaridine reductase from the opium poppy Papaver somniferum.
Authors: Higashi, Y. / Kutchan, T.M. / Smith, T.J.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Salutaridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8282
Polymers34,0831
Non-polymers7451
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.906, 139.906, 100.174
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Salutaridine reductase


Mass: 34082.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Production host: Escherichia coli (E. coli) / References: UniProt: Q071N0, salutaridine reductase (NADPH)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.15 Å3/Da / Density % sol: 70.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M MES pH 6.0-6.6, 1.9 M ammonium sulfate, 5%(v/v) PEG400, 0.1 M LiCl, 3%(v/v) glycerol. 2uL of 6 mg/ml SeMet SalR in addition of 4 mM NADPH was mixed with 2uL of the reservoir solution, ...Details: 0.1 M MES pH 6.0-6.6, 1.9 M ammonium sulfate, 5%(v/v) PEG400, 0.1 M LiCl, 3%(v/v) glycerol. 2uL of 6 mg/ml SeMet SalR in addition of 4 mM NADPH was mixed with 2uL of the reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9797 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 30, 2009
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.91→39 Å / Num. all: 45225 / Num. obs: 40176 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.279 / % possible all: 68

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.6.1_353refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.91→37.458 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0.13 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 2017 5.02 %
Rwork0.1926 --
obs0.1934 40173 88.87 %
all-45225 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.279 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6151 Å20 Å20 Å2
2---3.6151 Å2-0 Å2
3---7.2302 Å2
Refinement stepCycle: LAST / Resolution: 1.91→37.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 48 286 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072346
X-RAY DIFFRACTIONf_angle_d1.0773184
X-RAY DIFFRACTIONf_dihedral_angle_d15.649900
X-RAY DIFFRACTIONf_chiral_restr0.069360
X-RAY DIFFRACTIONf_plane_restr0.005407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9101-1.97840.21731440.21742907X-RAY DIFFRACTION69
1.9784-2.05760.24241760.20763137X-RAY DIFFRACTION75
2.0576-2.15120.24111850.20293210X-RAY DIFFRACTION76
2.1512-2.26460.23611970.20843815X-RAY DIFFRACTION90
2.2646-2.40650.21962190.19713903X-RAY DIFFRACTION92
2.4065-2.59220.23082100.19333997X-RAY DIFFRACTION94
2.5922-2.8530.19242180.19054105X-RAY DIFFRACTION96
2.853-3.26570.21812150.19754205X-RAY DIFFRACTION98
3.2657-4.11360.18662270.17114314X-RAY DIFFRACTION99
4.1136-37.46480.19412260.1924563X-RAY DIFFRACTION99

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