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- PDB-7cs6: IiPLR1 with NADP+ and (-)lariciresinol -

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Basic information

Entry
Database: PDB / ID: 7cs6
TitleIiPLR1 with NADP+ and (-)lariciresinol
ComponentsPinoresinol-lariciresinol reductase
KeywordsOXIDOREDUCTASE / IiPLR1 / NADP+ / lariciresinol / PLANT PROTEIN
Function / homology
Function and homology information


pinoresinol reductase activity / lignan biosynthetic process / nucleotide binding
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-lariciresinol reductase
Similarity search - Component
Biological speciesIsatis tinctoria (woad)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20139658355 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-lariciresinol reductase
B: Pinoresinol-lariciresinol reductase
C: Pinoresinol-lariciresinol reductase
D: Pinoresinol-lariciresinol reductase
E: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,61018
Polymers213,9766
Non-polymers6,63512
Water12,376687
1
A: Pinoresinol-lariciresinol reductase
hetero molecules

C: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5376
Polymers71,3252
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x+y-1,-x,z-1/31
Buried area4900 Å2
ΔGint-13 kcal/mol
Surface area24640 Å2
MethodPISA
2
B: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5376
Polymers71,3252
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-16 kcal/mol
Surface area25450 Å2
MethodPISA
3
D: Pinoresinol-lariciresinol reductase
E: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5376
Polymers71,3252
Non-polymers2,2124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-14 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.441, 244.441, 75.641
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein
Pinoresinol-lariciresinol reductase / IiPLR1


Mass: 35662.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Isatis tinctoria (woad) / Production host: Escherichia coli (E. coli) / References: UniProt: I6LRS1
#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.: 687 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2M sodium citrate tribasic, 0.1 M sodium citrate/citric acid, pH 4.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / 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: 2.2→42.34 Å / Num. obs: 130416 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 35.4461524601 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 24.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.858 / Num. unique obs: 12796

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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: 2.20139658355→42.3384231453 Å / SU ML: 0.257504258093 / Cross valid method: FREE R-VALUE / σ(F): 1.34264220368 / Phase error: 26.6275431501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.240029316432 2003 1.5358780499 %
Rwork0.197430928643 128411 -
obs0.198087564542 130414 99.6553700378 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.0748317833 Å2
Refinement stepCycle: LAST / Resolution: 2.20139658355→42.3384231453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13975 0 156 687 14818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074553458082814397
X-RAY DIFFRACTIONf_angle_d1.361706134319511
X-RAY DIFFRACTIONf_chiral_restr0.06709454541972213
X-RAY DIFFRACTIONf_plane_restr0.004663859854522437
X-RAY DIFFRACTIONf_dihedral_angle_d16.0850003038539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2014-2.25640.3373702479831390.2918076279428923X-RAY DIFFRACTION97.745658505
2.2564-2.31740.2996369782321420.267669110429149X-RAY DIFFRACTION99.6995385771
2.3174-2.38560.3325876612071380.2538660826429089X-RAY DIFFRACTION99.6436285097
2.3856-2.46260.3020572119041440.2497163233719157X-RAY DIFFRACTION99.6678096871
2.4626-2.55060.2892459680181430.2394299433919116X-RAY DIFFRACTION99.7737068966
2.5506-2.65270.2922749123421450.2311753173449124X-RAY DIFFRACTION99.7954349699
2.6527-2.77350.3184930885891430.2250648664549170X-RAY DIFFRACTION99.7750160703
2.7735-2.91960.2376744797721410.2182467648389143X-RAY DIFFRACTION99.7421572841
2.9196-3.10250.2458426565291420.2088007405079163X-RAY DIFFRACTION99.871203177
3.1025-3.3420.2359385356111440.2037563582839198X-RAY DIFFRACTION99.9358151476
3.342-3.67810.2383380922961430.1870023651119201X-RAY DIFFRACTION99.9251416961
3.6781-4.20990.22565345311400.1710180154989263X-RAY DIFFRACTION99.9362312679
4.2099-5.30250.1981701990681490.1563359396459277X-RAY DIFFRACTION99.9363867684
5.3025-42.33840.199573654261500.1766389297759438X-RAY DIFFRACTION99.7295610568

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