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

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Basic information

Entry
Database: PDB / ID: 1qyc
TitleCrystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases, and their relationship to isoflavone reductases
Componentsphenylcoumaran benzylic ether reductase PT1
KeywordsPLANT PROTEIN / NADPH-dependent aromatic alcohol reductases / PCBER / PLR / IFR / lignans / isoflavonoids
Function / homology
Function and homology information


Oxidoreductases; Reducing C-O-C group as acceptor; With NADH or NADPH as donor / lignan biosynthetic process / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor
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
Phenylcoumaran benzylic ether reductase PT1
Similarity search - Component
Biological speciesPinus taeda (loblolly pine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 2.2 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: phenylcoumaran benzylic ether reductase PT1
B: phenylcoumaran benzylic ether reductase PT1


Theoretical massNumber of molelcules
Total (without water)67,1262
Polymers67,1262
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-19 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.195, 67.941, 75.019
Angle α, β, γ (deg.)90.00, 115.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein phenylcoumaran benzylic ether reductase PT1


Mass: 33563.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pinus taeda (loblolly pine) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9LL41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Na cacodylate, Na citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG80001reservoir
20.1 Msodium cacodylate1reservoir
30.2 Msodium citrate1reservoir
420 mMTris1droppH8.0
51 mMEDTA1drop
65 mMdithiothreitol1drop
750 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2002
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. all: 26284 / Num. obs: 26284 / % possible obs: 98 % / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 144316

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALAdata scaling
SOLVE/ RESOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD, MIR / Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1291 5 %random
Rwork0.195 ---
all0.249 26284 --
obs0.226 24993 --
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 0 291 5011
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.91
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS

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