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- PDB-7cs2: Apo structure of dimeric IiPLR1 -

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Basic information

Entry
Database: PDB / ID: 7cs2
TitleApo structure of dimeric IiPLR1
ComponentsPinoresinol-lariciresinol reductase
KeywordsOXIDOREDUCTASE / PLR1 / dimer / PLANT PROTEIN
Function / homologypinoresinol reductase activity / Phenylcoumaran benzylic ether reductase-like / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily / Pinoresinol-lariciresinol reductase
Function and homology information
Biological speciesIsatis tinctoria (woad)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68800468428 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
C: Pinoresinol-lariciresinol reductase
B: Pinoresinol-lariciresinol reductase
D: Pinoresinol-lariciresinol reductase
E: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)213,9766
Polymers213,9766
Non-polymers00
Water1,63991
1
A: Pinoresinol-lariciresinol reductase
C: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,3252
Polymers71,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area25410 Å2
MethodPISA
2
B: Pinoresinol-lariciresinol reductase
D: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,3252
Polymers71,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-7 kcal/mol
Surface area25590 Å2
MethodPISA
3
E: Pinoresinol-lariciresinol reductase
F: Pinoresinol-lariciresinol reductase


Theoretical massNumber of molelcules
Total (without water)71,3252
Polymers71,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-8 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.758, 242.458, 77.562
Angle α, β, γ (deg.)90.000, 110.532, 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-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.81 %
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: 2.688→31.399 Å / Num. obs: 70443 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 66.1630245508 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.8
Reflection shellResolution: 2.69→2.78 Å / Rmerge(I) obs: 0.764 / Num. unique obs: 6742

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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: 2.68800468428→31.3980458407 Å / SU ML: 0.348769881523 / Cross valid method: FREE R-VALUE / σ(F): 1.35349369364 / Phase error: 26.4830188047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241548783356 1996 2.83349658589 %
Rwork0.200523743192 68447 -
obs0.201731584446 70443 98.9645967969 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.4566911034 Å2
Refinement stepCycle: LAST / Resolution: 2.68800468428→31.3980458407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13755 0 0 91 13846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010149096729513992
X-RAY DIFFRACTIONf_angle_d1.1558747658718903
X-RAY DIFFRACTIONf_chiral_restr0.06116862907372165
X-RAY DIFFRACTIONf_plane_restr0.006054269574772413
X-RAY DIFFRACTIONf_dihedral_angle_d16.71929858444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.688005-2.75520.3169591835071340.2633153192424612X-RAY DIFFRACTION93.2783018868
2.7552-2.82960.2905842671131380.2673958270314856X-RAY DIFFRACTION99.5217218015
2.8296-2.91280.3542812311051490.2574532717884927X-RAY DIFFRACTION99.587992937
2.9128-3.00680.2716464442651400.2419585118094896X-RAY DIFFRACTION99.6044303797
3.0068-3.11420.2966574194061450.2411501950134937X-RAY DIFFRACTION99.6275240149
3.1142-3.23870.3028519095751440.2542521405894926X-RAY DIFFRACTION99.6266457064
3.2387-3.3860.298113306761470.2385542685844940X-RAY DIFFRACTION99.725544011
3.386-3.56420.2978295511451370.2363672266964829X-RAY DIFFRACTION98.590430812
3.5642-3.78720.2732180905431380.212253162184899X-RAY DIFFRACTION99.2903607333
3.7872-4.0790.188839081931420.2011590412274880X-RAY DIFFRACTION98.5478806907
4.079-4.48850.1948008958131450.1628938912594923X-RAY DIFFRACTION99.8620689655
4.4885-5.13550.2415338204461450.1639628726494963X-RAY DIFFRACTION99.9217527387
5.1355-6.4610.2384368596911450.1939366079024948X-RAY DIFFRACTION99.7649363369
6.461-31.398040.1974474525771470.1719716412764911X-RAY DIFFRACTION98.5580670304

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