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- PDB-7csh: AtPrR2 with NADP+ and (+)pinoresinol -

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Basic information

Entry
Database: PDB / ID: 7csh
TitleAtPrR2 with NADP+ and (+)pinoresinol
ComponentsPinoresinol reductase 2
KeywordsOXIDOREDUCTASE / AtPrR2 / NADP+ / (+)pinoresinol / PLANT PROTEIN
Function / homology
Function and homology information


(-)-pinoresinol reductase / lignan biosynthetic process / pinoresinol reductase activity / plasmodesma
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 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59077503881 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
A: Pinoresinol reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5663
Polymers35,4621
Non-polymers1,1042
Water9,224512
1
A: Pinoresinol reductase 2
hetero molecules

A: Pinoresinol reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1326
Polymers70,9252
Non-polymers2,2084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5360 Å2
ΔGint-18 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.001, 90.465, 117.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-920-

HOH

21A-973-

HOH

31A-996-

HOH

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Components

#1: Protein Pinoresinol reductase 2 / AtPrR2 / (-)-pinoresinol reductase / Pinoresinol-lariciresinol reductase 2 / AtPLR2


Mass: 35462.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRR2, PLR2, At4g13660, F18A5.50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SVP6, (-)-pinoresinol reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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 / Pinoresinol


Mass: 358.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL malic acid, pH 7.0

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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: 1.59→39.001 Å / Num. obs: 55657 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.9230290314 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 20.7
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 0.475 / Num. unique obs: 5475

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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: 1.59077503881→39.0005 Å / SU ML: 0.100466840733 / Cross valid method: FREE R-VALUE / σ(F): 1.34366837069 / Phase error: 16.7727272879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183481709616 1999 3.59164166232 %
Rwork0.155820890259 53658 -
obs0.156809859231 55657 99.3679812894 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.0389862033 Å2
Refinement stepCycle: LAST / Resolution: 1.59077503881→39.0005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 74 512 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055097255692580
X-RAY DIFFRACTIONf_angle_d1.16053433043498
X-RAY DIFFRACTIONf_chiral_restr0.0638065363167388
X-RAY DIFFRACTIONf_plane_restr0.00510883361507441
X-RAY DIFFRACTIONf_dihedral_angle_d15.40545595841521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5908-1.63060.2120491721021390.1899196315523728X-RAY DIFFRACTION98.1472081218
1.6306-1.67460.2006188715741420.1768741325343818X-RAY DIFFRACTION99.9495204442
1.6746-1.72390.1841142859811410.1668941092223791X-RAY DIFFRACTION99.872999746
1.7239-1.77960.2003143633171430.1699290999443826X-RAY DIFFRACTION99.7737556561
1.7796-1.84320.1851247092031400.1615117686173781X-RAY DIFFRACTION98.8653555219
1.8432-1.9170.1909601380851430.1558520024413821X-RAY DIFFRACTION100
1.917-2.00420.1863432175131430.1568964969513843X-RAY DIFFRACTION99.9749184851
2.0042-2.10990.1839155724941430.1535575985123828X-RAY DIFFRACTION99.8993710692
2.1099-2.2420.1907892645711420.159577966323826X-RAY DIFFRACTION99.2992992993
2.242-2.41510.1732068201591430.1551490574073834X-RAY DIFFRACTION99.9497361146
2.4151-2.65810.1809150693521450.1555579707943880X-RAY DIFFRACTION99.9751614506
2.6581-3.04260.1765907293261430.1637951820753855X-RAY DIFFRACTION99.5270102066
3.0426-3.83290.1782637550151460.1469624494983913X-RAY DIFFRACTION99.7787610619
3.8329-39.00050.180777230981460.1433394523723914X-RAY DIFFRACTION96.3455149502

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