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- PDB-7csf: AtPrR1 with NADP+ and (-)secoisolariciresinol -

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Basic information

Entry
Database: PDB / ID: 7csf
TitleAtPrR1 with NADP+ and (-)secoisolariciresinol
ComponentsPinoresinol reductase 1
KeywordsOXIDOREDUCTASE / AtPrR1 / NADP+ / (-)secoisolariciresinol / 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-GO6 / Chem-NDP / Pinoresinol reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98241803828 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)146,81112
Polymers142,3794
Non-polymers4,4318
Water15,223845
1
C: Pinoresinol reductase 1
D: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4056
Polymers71,1902
Non-polymers2,2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-14 kcal/mol
Surface area24630 Å2
MethodPISA
2
A: Pinoresinol reductase 1
B: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4056
Polymers71,1902
Non-polymers2,2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-17 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.127, 143.273, 77.066
Angle α, β, γ (deg.)90.000, 116.376, 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-GO6 / (2R,3R)-2,3-bis[(3-methoxy-4-oxidanyl-phenyl)methyl]butane-1,4-diol / (-)-secoisolariciresinol


Mass: 362.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26O6 / 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.: 845 / 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: 2.58 Å3/Da / Density % sol: 52.23 %
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: 1.98→39.84 Å / Num. obs: 99396 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.3185106675 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 25.5
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 1.06 / Num. unique obs: 9769

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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: 1.98241803828→38.3966649277 Å / SU ML: 0.196055566634 / Cross valid method: FREE R-VALUE / σ(F): 1.34361456234 / Phase error: 23.0397762793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218598194837 2032 2.044368429 %
Rwork0.177749103211 97363 -
obs0.178584437499 99395 99.8262493974 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.5893692364 Å2
Refinement stepCycle: LAST / Resolution: 1.98241803828→38.3966649277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9944 0 104 845 10893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074267863805710268
X-RAY DIFFRACTIONf_angle_d0.98304418662213928
X-RAY DIFFRACTIONf_chiral_restr0.05306107125571552
X-RAY DIFFRACTIONf_plane_restr0.00470127426971764
X-RAY DIFFRACTIONf_dihedral_angle_d13.62854048846072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98242-2.02850.329555441011170.2615092217296359X-RAY DIFFRACTION97.9727685325
2.0285-2.07930.280312399231460.2322480135566479X-RAY DIFFRACTION99.9849079384
2.0793-2.13550.2549242336521350.2124257475636467X-RAY DIFFRACTION100
2.1355-2.19830.2595732102521430.209570595396490X-RAY DIFFRACTION100
2.1983-2.26920.2557693978741150.1983013528386518X-RAY DIFFRACTION100
2.2692-2.35030.2329906473931450.1916681425386461X-RAY DIFFRACTION100
2.3503-2.44440.2455003389311390.1957791116466471X-RAY DIFFRACTION100
2.4444-2.55570.244890075261410.1949712183186524X-RAY DIFFRACTION99.9849984998
2.5557-2.69040.2644868129831370.1915897004066455X-RAY DIFFRACTION100
2.6904-2.85890.2484789088521390.1963997053916536X-RAY DIFFRACTION100
2.8589-3.07950.2318758038951270.1915585693366505X-RAY DIFFRACTION99.9397227245
3.0795-3.38930.2711524169951280.1885684696746484X-RAY DIFFRACTION99.9093381686
3.3893-3.87930.1676404279151380.1637337440646520X-RAY DIFFRACTION99.9249587273
3.8793-4.88590.1810154368771440.1406539500676513X-RAY DIFFRACTION99.9699654603
4.8859-38.39666490.1793789987551380.1528024950376581X-RAY DIFFRACTION99.7032200623

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