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- PDB-1qyd: Crystal structures of pinoresinol-lariciresinol and phenylcoumara... -

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Basic information

Entry
Database: PDB / ID: 1qyd
TitleCrystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases, and their relationship to isoflavone reductases
Componentspinoresinol-lariciresinol reductase
KeywordsPLANT PROTEIN / NADPH-dependent aromatic alcohol reductases / PCBER / PLR / IFR / lignans / isoflavonoids
Function / homology
Function and homology information


(-)-lariciresinol reductase / lariciresinol reductase activity / (-)-pinoresinol catabolic process / (+)-pinoresinol catabolic process / (-)-lariciresinol catabolic process / (-)-lariciresinol biosynthetic process / (+)-lariciresinol biosynthetic process / (+)-secoisolariciresinol biosynthetic process / (+)-pinoresinol reductase / (-)-pinoresinol reductase ...(-)-lariciresinol reductase / lariciresinol reductase activity / (-)-pinoresinol catabolic process / (+)-pinoresinol catabolic process / (-)-lariciresinol catabolic process / (-)-lariciresinol biosynthetic process / (+)-lariciresinol biosynthetic process / (+)-secoisolariciresinol biosynthetic process / (+)-pinoresinol reductase / (-)-pinoresinol reductase / pinoresinol reductase activity / lignan biosynthetic process
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional pinoresinol-lariciresinol reductase 1
Similarity search - Component
Biological speciesThuja plicata (western redcedar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMin, T. / Kasahara, H. / Bedgar, D.L. / Youn, B. / Lawrence, P.K. / Gang, D.R. / Halls, S.C. / Park, H. / Hilsenbeck, J.L. / Davin, L.B. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases.
Authors: Min, T. / Kasahara, H. / Bedgar, D.L. / Youn, B. / Lawrence, P.K. / Gang, D.R. / Halls, S.C. / Park, H. / Hilsenbeck, J.L. / Davin, L.B. / Lewis, N.G. / Kang, C.
History
DepositionSep 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pinoresinol-lariciresinol reductase
B: pinoresinol-lariciresinol reductase
C: pinoresinol-lariciresinol reductase
D: pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)142,4964
Polymers142,4964
Non-polymers00
Water1,53185
1
A: pinoresinol-lariciresinol reductase
C: pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,2482
Polymers71,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pinoresinol-lariciresinol reductase
D: pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,2482
Polymers71,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.574, 125.959, 128.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
pinoresinol-lariciresinol reductase


Mass: 35624.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thuja plicata (western redcedar) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9LD14
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, MES, NaCl, Ca Acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %PEG80001reservoir
20.1 MMES1reservoirpH6.2
30.1 M1reservoirNaCl
40.1 Mcalcium acetate1reservoir
520 mMTris1droppH8.0
61 mMEDTA1drop
75 mMdithiothreitol1drop
850 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 33210 / Num. obs: 33210 / % possible obs: 79 % / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 36439

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1681 5 %RANDOM
Rwork0.193 ---
all0.251 33210 --
obs0.235 31529 --
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9987 0 0 85 10072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg3.54
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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