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- PDB-7csb: AtPrR1 with NADP+ and (+)pinoresinol -

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Basic information

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


(+)-pinoresinol reductase / (-)-pinoresinol reductase / pinoresinol reductase activity / lignan biosynthetic process
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-GEC / Chem-NDP / Pinoresinol reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00201707558 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)146,79512
Polymers142,3794
Non-polymers4,4158
Water10,269570
1
C: Pinoresinol reductase 1
D: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3976
Polymers71,1902
Non-polymers2,2084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-16 kcal/mol
Surface area24650 Å2
MethodPISA
2
A: Pinoresinol reductase 1
B: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3976
Polymers71,1902
Non-polymers2,2084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-18 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.156, 144.716, 77.021
Angle α, β, γ (deg.)90.000, 116.288, 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-GEC / 4-[(3S,3aR,6S,6aR)-6-(3-methoxy-4-oxidanyl-phenyl)-1,3,3a,4,6,6a-hexahydrofuro[3,4-c]furan-3-yl]-2-methoxy-phenol / (+)-pinoresinol


Mass: 358.385 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22O6
#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.: 570 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
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: 2→33.9 Å / Num. obs: 86455 / % possible obs: 89.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.7558578063 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 24.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.719 / Num. unique obs: 9547

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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: 2.00201707558→33.8996723974 Å / SU ML: 0.256478885961 / Cross valid method: FREE R-VALUE / σ(F): 1.33465144116 / Phase error: 28.4807732621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239076218895 1996 2.30876892647 %
Rwork0.200204383347 84457 -
obs0.20112262014 86453 88.4972873375 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.8347900471 Å2
Refinement stepCycle: LAST / Resolution: 2.00201707558→33.8996723974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9935 0 104 570 10609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014341505845910267
X-RAY DIFFRACTIONf_angle_d1.8830816434413941
X-RAY DIFFRACTIONf_chiral_restr0.120032809771559
X-RAY DIFFRACTIONf_plane_restr0.006459329494761763
X-RAY DIFFRACTIONf_dihedral_angle_d14.5210083536109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0020171-2.05210.3518326059981600.2772022562686615X-RAY DIFFRACTION97.4119338605
2.0521-2.10760.2936928050331630.2696853322726777X-RAY DIFFRACTION99.9855928541
2.1076-2.16960.3364620722511640.2658201930066796X-RAY DIFFRACTION99.9138673557
2.1696-2.23960.386722263249930.3375735188313981X-RAY DIFFRACTION59.4050743657
2.2396-2.31960.330635348438740.3212768323273034X-RAY DIFFRACTION44.5655291081
2.3196-2.41240.3173296187831710.2443596187216817X-RAY DIFFRACTION99.9142121819
2.4124-2.52220.2705938325221490.2417367145176785X-RAY DIFFRACTION99.9135446686
2.5222-2.65510.2839318474431620.2296145178096837X-RAY DIFFRACTION99.9428816222
2.6551-2.82140.3218467204141640.231638604536771X-RAY DIFFRACTION99.9279538905
2.8214-3.03910.2622744693781540.223945652356809X-RAY DIFFRACTION99.8709122203
3.0391-3.34470.2410174879661660.2191757451476832X-RAY DIFFRACTION99.8430589242
3.3447-3.82810.238984992901770.1993631660353902X-RAY DIFFRACTION57.005730659
3.8281-4.82080.1793693161551420.1461657352565624X-RAY DIFFRACTION82.1484541958
4.8208-33.899670.1692774250311570.1425315660386877X-RAY DIFFRACTION99.5612172682

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