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

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Basic information

Entry
Database: PDB / ID: 7csc
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-GEF / Chem-NDP / Pinoresinol reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51511848629 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
E: Pinoresinol reductase 1
F: Pinoresinol reductase 1
A: Pinoresinol reductase 1
B: Pinoresinol reductase 1
C: Pinoresinol reductase 1
D: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,19218
Polymers213,5696
Non-polymers6,62312
Water3,477193
1
E: Pinoresinol reductase 1
F: 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 area4790 Å2
ΔGint-16 kcal/mol
Surface area24740 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 area4760 Å2
ΔGint-17 kcal/mol
Surface area24890 Å2
MethodPISA
3
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 area4880 Å2
ΔGint-16 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.015, 128.712, 105.323
Angle α, β, γ (deg.)90.000, 91.947, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,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.: 6
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-GEF / 4-[(3R,3aS,6R,6aS)-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.: 6 / Source method: obtained synthetically / Formula: C20H22O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M sodium malonate, pH 6.0, 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: 2.515→10.098 Å / Num. obs: 92982 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 44.5335997663 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.7
Reflection shellResolution: 2.52→2.6 Å / Rmerge(I) obs: 0.939 / Num. unique obs: 8665

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Processing

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

1qyd


Resolution: 2.51511848629→10.097232232 Å / SU ML: 0.314565897283 / Cross valid method: FREE R-VALUE / σ(F): 1.34368726089 / Phase error: 27.2295659082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246962162661 1958 2.10578391517 %
Rwork0.208653901692 91024 -
obs0.209483534947 92982 98.9875762512 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.2300998447 Å2
Refinement stepCycle: LAST / Resolution: 2.51511848629→10.097232232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14887 0 156 193 15236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012021777930115384
X-RAY DIFFRACTIONf_angle_d1.6942272914420888
X-RAY DIFFRACTIONf_chiral_restr0.08302554782182339
X-RAY DIFFRACTIONf_plane_restr0.006229453625252638
X-RAY DIFFRACTIONf_dihedral_angle_d16.08083556379152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51512-2.5770.3954973756691270.3021414379745922X-RAY DIFFRACTION90.0550841149
2.577-2.64550.3123382100341580.2889522306156446X-RAY DIFFRACTION99.5327807084
2.6455-2.72180.366778819111310.2829964727636510X-RAY DIFFRACTION99.4012872325
2.7218-2.80790.2901942730851490.270992164986561X-RAY DIFFRACTION99.6435996436
2.8079-2.90590.3000676654221470.2650871689286463X-RAY DIFFRACTION99.6081977095
2.9059-3.01930.3179982728321470.2589630043566586X-RAY DIFFRACTION99.7333728337
3.0193-3.15270.2859097527771330.2557113902826510X-RAY DIFFRACTION99.6848739496
3.1527-3.31330.2922592145371340.2370683530456546X-RAY DIFFRACTION99.7759522031
3.3133-3.51270.2722043804981350.2224049171866582X-RAY DIFFRACTION99.7623644735
3.5127-3.77070.2207816321371510.2016490066326535X-RAY DIFFRACTION99.8059411853
3.7707-4.12650.2304006636551460.1888387799336559X-RAY DIFFRACTION99.7916356601
4.1265-4.67110.2021142905881360.1693998243376545X-RAY DIFFRACTION99.6717887513
4.6711-5.70290.2054688130621280.1734379431656606X-RAY DIFFRACTION99.6006507913
5.7029-10.09720.1892239125231360.1543067028216653X-RAY DIFFRACTION99.7648787656

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