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- PDB-7cs8: IiPLR1 with NADP+ and (-)secoisolariciresinol -

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Basic information

Entry
Database: PDB / ID: 7cs8
TitleIiPLR1 with NADP+ and (-)secoisolariciresinol
ComponentsPinoresinol-lariciresinol reductase
KeywordsOXIDOREDUCTASE / IiPLR1 / NADP+ / secoisolariciresinol / PLANT PROTEIN
Function / homology
Function and homology information


pinoresinol reductase activity / 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-GO6 / Chem-NDP / Pinoresinol-lariciresinol reductase
Similarity search - Component
Biological speciesIsatis tinctoria (woad)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.60003253525 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

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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)220,62318
Polymers213,9766
Non-polymers6,64712
Water1,76598
1
A: Pinoresinol-lariciresinol reductase
hetero molecules

C: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5416
Polymers71,3252
Non-polymers2,2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area4740 Å2
ΔGint-17 kcal/mol
Surface area24950 Å2
MethodPISA
2
B: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5416
Polymers71,3252
Non-polymers2,2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-10 kcal/mol
Surface area25280 Å2
MethodPISA
3
D: Pinoresinol-lariciresinol reductase
E: Pinoresinol-lariciresinol reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5416
Polymers71,3252
Non-polymers2,2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-12 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.363, 244.363, 76.029
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-GO6 / (2R,3R)-2,3-bis[(3-methoxy-4-oxidanyl-phenyl)methyl]butane-1,4-diol / (-)-secoisolariciresinol


Mass: 362.417 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
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: 2.6→40.73 Å / Num. obs: 80035 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 42.6726480012 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 16.3
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.368 / Num. unique obs: 7931

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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: 2.60003253525→40.7271666667 Å / SU ML: 0.490877523131 / Cross valid method: FREE R-VALUE / σ(F): 1.33793974778 / Phase error: 39.8350623438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.345594096466 1998 2.49799959992 %
Rwork0.276229908051 77986 -
obs0.277985370342 79984 99.9150552141 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.4759812713 Å2
Refinement stepCycle: LAST / Resolution: 2.60003253525→40.7271666667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13960 0 156 98 14214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008568829617314377
X-RAY DIFFRACTIONf_angle_d1.0934904398319473
X-RAY DIFFRACTIONf_chiral_restr0.05521355238112203
X-RAY DIFFRACTIONf_plane_restr0.0058589936682434
X-RAY DIFFRACTIONf_dihedral_angle_d17.87076869938480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.60003253525-2.6650.4017541569071370.331989851815505X-RAY DIFFRACTION99.805413055
2.665-2.73710.4010164230861430.3211188035675548X-RAY DIFFRACTION99.8771498771
2.7371-2.81760.3869818382971440.3270816391175535X-RAY DIFFRACTION99.8944591029
2.8176-2.90850.4113378196031360.3263375149645543X-RAY DIFFRACTION99.8066783831
2.9085-3.01240.3581474478061360.3155641236595527X-RAY DIFFRACTION99.9823446328
3.0124-3.1330.3958841769041420.3254484424395540X-RAY DIFFRACTION99.9472295515
3.133-3.27560.3753071070991430.3058045628075566X-RAY DIFFRACTION99.9474789916
3.2756-3.44820.3705747899391400.2822443219095545X-RAY DIFFRACTION99.9648320731
3.4482-3.66410.3183322426371420.2750991705125543X-RAY DIFFRACTION99.9648320731
3.6641-3.94680.3611892478141430.2683363060925592X-RAY DIFFRACTION99.9477169746
3.9468-4.34350.3426712694881460.2592750335375571X-RAY DIFFRACTION100
4.3435-4.97110.3332183111681470.2348143955665584X-RAY DIFFRACTION99.9476805023
4.9711-6.25940.3101877372881490.2667533492775643X-RAY DIFFRACTION100
6.2594-40.72716666670.297813414811500.2465823815365744X-RAY DIFFRACTION99.7461499408
Refinement TLS params.Method: refined / Origin x: -64.3631792763 Å / Origin y: 61.0704779999 Å / Origin z: -4.47347834531 Å
111213212223313233
T0.482237235275 Å20.010412025254 Å20.0196199012963 Å2-0.507878475421 Å2-0.00410690699484 Å2--0.470886289159 Å2
L0.157736721337 °2-0.111297855485 °20.0943759341971 °2--0.0146522821907 °2-0.0903031960018 °2--0.0164990874107 °2
S-0.0194545136951 Å °0.0144495899317 Å °0.0355083059617 Å °0.0221004561596 Å °-0.00711479151467 Å °-0.01748773727 Å °-0.0565130346979 Å °-0.0732909067286 Å °2.95821052496E-6 Å °
Refinement TLS groupSelection details: all

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