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- PDB-7csd: AtPrR1 with NADP+ and (+)lariciresinol -

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Basic information

Entry
Database: PDB / ID: 7csd
TitleAtPrR1 with NADP+ and (+)lariciresinol
ComponentsPinoresinol reductase 1
KeywordsOXIDOREDUCTASE / AtPrR1 / NADP+ / (+)lariciresinol / PLANT PROTEIN
Function / homology
Function and homology information


(+)-pinoresinol reductase / (-)-pinoresinol reductase / lignan biosynthetic process / pinoresinol reductase activity
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-GFU / Chem-NDP / Pinoresinol reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79709972859 Å
AuthorsShao, K. / Zhang, P.
CitationJournal: Nat Commun / Year: 2021
Title: Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases.
Authors: Xiao, Y. / Shao, K. / Zhou, J. / Wang, L. / Ma, X. / Wu, D. / Yang, Y. / Chen, J. / Feng, J. / Qiu, S. / Lv, Z. / Zhang, L. / Zhang, P. / Chen, W.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Pinoresinol reductase 1
D: Pinoresinol reductase 1
A: Pinoresinol reductase 1
B: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,80312
Polymers142,3794
Non-polymers4,4238
Water17,835990
1
C: Pinoresinol reductase 1
D: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4016
Polymers71,1902
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-20 kcal/mol
Surface area24040 Å2
MethodPISA
2
A: Pinoresinol reductase 1
B: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4016
Polymers71,1902
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-20 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.872, 143.671, 76.102
Angle α, β, γ (deg.)90.000, 116.331, 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
Pinoresinol reductase 1 / AtPrR1 / (+)-pinoresinol reductase / (-)-pinoresinol reductase / Pinoresinol-lariciresinol ...AtPrR1 / (+)-pinoresinol reductase / (-)-pinoresinol reductase / Pinoresinol-lariciresinol reductase 1 / AtPLR1


Mass: 35594.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRR1, PLR1, At1g32100, F3C3.10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FVQ6, (+)-pinoresinol reductase, (-)-pinoresinol reductase
#2: Chemical
ChemComp-GFU / 4-[[(3R,4R,5S)-4-(hydroxymethyl)-5-(3-methoxy-4-oxidanyl-phenyl)oxolan-3-yl]methyl]-2-methoxy-phenol / (+)-Lariciresinol


Mass: 360.401 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium fluoride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.797→34.642 Å / Num. obs: 129808 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.1572375186 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.857 / Num. unique obs: 11685

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QYD

1qyd


Resolution: 1.79709972859→34.641233627 Å / SU ML: 0.21122410403 / Cross valid method: FREE R-VALUE / σ(F): 1.34864890178 / Phase error: 24.8355954694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221742148856 2005 1.54458893134 %
Rwork0.185608171961 127803 -
obs0.186155082247 129808 98.5058090562 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.0484577379 Å2
Refinement stepCycle: LAST / Resolution: 1.79709972859→34.641233627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9931 0 104 990 11025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084472014129110259
X-RAY DIFFRACTIONf_angle_d1.5361266268813921
X-RAY DIFFRACTIONf_chiral_restr0.06167276126231551
X-RAY DIFFRACTIONf_plane_restr0.005092279974911763
X-RAY DIFFRACTIONf_dihedral_angle_d14.17347438836093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7971-1.8420.3134540680611310.2880861667347825X-RAY DIFFRACTION84.9183477426
1.842-1.89180.2957875680721290.2671522350949249X-RAY DIFFRACTION99.9254128929
1.8918-1.94750.2695565447061530.2509064928869202X-RAY DIFFRACTION99.8825539184
1.9475-2.01040.2719603841971280.2470150271829244X-RAY DIFFRACTION99.9253651775
2.0104-2.08220.2827892244471690.2319596922119261X-RAY DIFFRACTION99.8306161338
2.0822-2.16560.2532541180981300.2237981226519218X-RAY DIFFRACTION99.8397949375
2.1656-2.26410.2690393648671500.2228363140629210X-RAY DIFFRACTION99.7442455243
2.2641-2.38340.2592803747551550.2101991061619247X-RAY DIFFRACTION99.7136493796
2.3834-2.53270.2545467359311430.2076670432069211X-RAY DIFFRACTION99.5318152798
2.5327-2.72820.2597760700371490.2026634990399229X-RAY DIFFRACTION99.4802163997
2.7282-3.00260.2562405472131480.202607539549182X-RAY DIFFRACTION99.3398637138
3.0026-3.43680.2241944939471460.1921416341089229X-RAY DIFFRACTION99.0282032323
3.4368-4.32860.1995962402051350.1572408991999174X-RAY DIFFRACTION98.7901942057
4.3286-34.64120.1520122533141390.1381357445619322X-RAY DIFFRACTION99.1199580932

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