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- PDB-7cse: AtPrR1 with NADP+ and (-)lariciresinol -

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Basic information

Entry
Database: PDB / ID: 7cse
TitleAtPrR1 with NADP+ and (-)lariciresinol
ComponentsPinoresinol reductase 1
KeywordsOXIDOREDUCTASE / AtPrR1 / NADP+ / lariciresinol / 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-GFR / Chem-NDP / Pinoresinol reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4401905733 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)220,20418
Polymers213,5696
Non-polymers6,63512
Water8,269459
1
E: Pinoresinol reductase 1
F: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4016
Polymers71,1902
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-15 kcal/mol
Surface area24530 Å2
MethodPISA
2
A: Pinoresinol reductase 1
B: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4016
Polymers71,1902
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-17 kcal/mol
Surface area24790 Å2
MethodPISA
3
C: Pinoresinol reductase 1
D: Pinoresinol reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4016
Polymers71,1902
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-16 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.584, 129.486, 106.320
Angle α, β, γ (deg.)90.000, 90.758, 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-GFR / 4-[[(3S,4S,5R)-4-(hydroxymethyl)-5-(3-methoxy-4-oxidanyl-phenyl)oxolan-3-yl]methyl]-2-methoxy-phenol / (-)-Lariciresinol


Mass: 360.401 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H24O6 / 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.: 459 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
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: 2.44→47.752 Å / Num. obs: 106057 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 43.7933252506 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 22.6
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 1.082 / Num. unique obs: 10355

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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: 2.4401905733→47.7501931008 Å / SU ML: 0.258059460965 / Cross valid method: FREE R-VALUE / σ(F): 1.337501968 / Phase error: 24.4638691898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222489555799 1978 1.86505242513 %
Rwork0.18235972853 104078 -
obs0.183113307057 106056 99.6177075604 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.6600492891 Å2
Refinement stepCycle: LAST / Resolution: 2.4401905733→47.7501931008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14887 0 156 459 15502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00902277959815378
X-RAY DIFFRACTIONf_angle_d1.398237835520870
X-RAY DIFFRACTIONf_chiral_restr0.06563935224252333
X-RAY DIFFRACTIONf_plane_restr0.0052038710542638
X-RAY DIFFRACTIONf_dihedral_angle_d16.05603024899140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4402-2.50120.2597580109161410.2335132652237156X-RAY DIFFRACTION96.0890176455
2.5012-2.56880.3197744717131310.246959884387444X-RAY DIFFRACTION99.9868004224
2.5688-2.64440.3040253814411540.2458860905457417X-RAY DIFFRACTION99.9603908107
2.6444-2.72980.2983010851451560.2482010590587403X-RAY DIFFRACTION99.8415004623
2.7298-2.82730.3029661222781210.2270243964177446X-RAY DIFFRACTION99.9471668208
2.8273-2.94050.2838827295451490.218800093747448X-RAY DIFFRACTION99.9473753453
2.9405-3.07430.2608052442551380.2152465948167410X-RAY DIFFRACTION99.9602701629
3.0743-3.23640.2584562651781370.2153356265447468X-RAY DIFFRACTION100
3.2364-3.43910.2201214100661450.2052223179977458X-RAY DIFFRACTION99.9737015122
3.4391-3.70450.233535196531370.1849539937727435X-RAY DIFFRACTION99.9340108222
3.7045-4.07710.2064319263171370.1720582283537469X-RAY DIFFRACTION99.8424783408
4.0771-4.66670.1691418956541440.1470257662097466X-RAY DIFFRACTION99.9212184874
4.6667-5.87780.2096469208431480.154145187927506X-RAY DIFFRACTION99.8825525251
5.8778-47.7501930.1595518691151400.1374542397997552X-RAY DIFFRACTION99.3798449612

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