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- PDB-7cs9: AtPrR1 in apo form -

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Basic information

Entry
Database: PDB / ID: 7cs9
TitleAtPrR1 in apo form
ComponentsPinoresinol reductase 1
KeywordsOXIDOREDUCTASE / AtPrR1 / dimer / 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
Pinoresinol reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80114138241 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
B: Pinoresinol reductase 1
C: Pinoresinol reductase 1
A: Pinoresinol reductase 1
D: Pinoresinol reductase 1


Theoretical massNumber of molelcules
Total (without water)142,3794
Polymers142,3794
Non-polymers00
Water00
1
B: Pinoresinol reductase 1
C: Pinoresinol reductase 1


Theoretical massNumber of molelcules
Total (without water)71,1902
Polymers71,1902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pinoresinol reductase 1
D: Pinoresinol reductase 1


Theoretical massNumber of molelcules
Total (without water)71,1902
Polymers71,1902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.727, 134.916, 142.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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

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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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.8→39.271 Å / Num. obs: 39296 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 58.8908106247 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 19.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.283 / Num. unique obs: 3860

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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: 2.80114138241→39.270799393 Å / SU ML: 0.432085596789 / Cross valid method: FREE R-VALUE / σ(F): 1.32663843817 / Phase error: 33.0036151099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.280390883277 2000 5.08957654723 %
Rwork0.221104640091 37296 -
obs0.224245118234 39296 99.8754606684 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.4159313122 Å2
Refinement stepCycle: LAST / Resolution: 2.80114138241→39.270799393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9564 0 0 0 9564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01087421887559752
X-RAY DIFFRACTIONf_angle_d1.2930561739413190
X-RAY DIFFRACTIONf_chiral_restr0.06539866176261487
X-RAY DIFFRACTIONf_plane_restr0.007658223715811707
X-RAY DIFFRACTIONf_dihedral_angle_d16.27069837095910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8012-2.87120.3623945470761440.2947507875612613X-RAY DIFFRACTION99.6746203905
2.8712-2.94880.3591408643721320.3051510410562620X-RAY DIFFRACTION99.7101449275
2.9488-3.03550.3433751972851530.3030901145222636X-RAY DIFFRACTION99.9641577061
3.0355-3.13350.35604707671370.2930346332972610X-RAY DIFFRACTION100
3.1335-3.24540.3910599811031400.2861606616382619X-RAY DIFFRACTION99.8913830558
3.2454-3.37530.3475002061191410.2736127584342660X-RAY DIFFRACTION99.9286478773
3.3753-3.52880.372570584581410.2578055192062638X-RAY DIFFRACTION100
3.5288-3.71470.3297125455141420.255166794152655X-RAY DIFFRACTION100
3.7147-3.94720.3377577164241380.2328808896062656X-RAY DIFFRACTION99.9284692418
3.9472-4.25170.2740884281451420.2067174290892670X-RAY DIFFRACTION100
4.2517-4.67890.2178334480391480.1747935787722660X-RAY DIFFRACTION100
4.6789-5.35450.2466334429011420.1863660188952693X-RAY DIFFRACTION99.9647390691
5.3545-6.74060.2810664003531450.2038681184752736X-RAY DIFFRACTION99.9653018737
6.7406-39.27070.1821548259671550.1701602567852830X-RAY DIFFRACTION99.2683737945

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