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- PDB-7csg: AtPrR2 in apo form -

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Basic information

Entry
Database: PDB / ID: 7csg
TitleAtPrR2 in apo form
ComponentsPinoresinol reductase 2
KeywordsOXIDOREDUCTASE / AtPrR2 / homodimer / PLANT PROTEIN
Function / homology
Function and homology information


(-)-pinoresinol reductase / pinoresinol reductase activity / lignan biosynthetic process / plasmodesma
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 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99689386689 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 reductase 2
B: Pinoresinol reductase 2


Theoretical massNumber of molelcules
Total (without water)70,9252
Polymers70,9252
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.291, 57.936, 71.559
Angle α, β, γ (deg.)107.318, 95.772, 113.244
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Pinoresinol reductase 2 / AtPrR2 / (-)-pinoresinol reductase / Pinoresinol-lariciresinol reductase 2 / AtPLR2


Mass: 35462.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRR2, PLR2, At4g13660, F18A5.50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SVP6, (-)-pinoresinol reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M magnesium chloride, 0.1 M sodium HEPES, pH 7.5, 25% 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: 1.996→34.162 Å / Num. obs: 39962 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.5003133031 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 24.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.422 / Num. unique obs: 3909

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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: 1.99689386689→34.1611618469 Å / SU ML: 0.217670236234 / Cross valid method: FREE R-VALUE / σ(F): 1.98030952507 / Phase error: 24.6104888862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237839461351 2001 5.00725689405 %
Rwork0.188831385123 37961 -
obs0.191275975048 39962 97.4065226929 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.1118130414 Å2
Refinement stepCycle: LAST / Resolution: 1.99689386689→34.1611618469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 0 378 4831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006970833258954531
X-RAY DIFFRACTIONf_angle_d0.8018029766586114
X-RAY DIFFRACTIONf_chiral_restr0.0543089761307696
X-RAY DIFFRACTIONf_plane_restr0.0045738145012779
X-RAY DIFFRACTIONf_dihedral_angle_d14.53701852962717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9969-2.04680.2428286469581440.2060023520322654X-RAY DIFFRACTION95.0407608696
2.0468-2.10220.3089412542541430.1988978936412692X-RAY DIFFRACTION97.022587269
2.1022-2.1640.2761200382691370.1966426415562688X-RAY DIFFRACTION96.9790593889
2.164-2.23380.2513081862881340.1991128023642742X-RAY DIFFRACTION97.4254742547
2.2338-2.31370.2533927252791580.1944551215892715X-RAY DIFFRACTION97.7543382103
2.3137-2.40630.2419478542991290.1943395427442713X-RAY DIFFRACTION97.6296805222
2.4063-2.51580.2881585660581620.1974001166262700X-RAY DIFFRACTION97.7125298737
2.5158-2.64830.2468600875941350.1953209399272738X-RAY DIFFRACTION98.02115319
2.6483-2.81420.2504696161961470.1976049966942712X-RAY DIFFRACTION98.2811962874
2.8142-3.03140.2372636193181410.1929888930582754X-RAY DIFFRACTION98.1688708037
3.0314-3.33620.2234655120871460.1953260749682734X-RAY DIFFRACTION98.2599795292
3.3362-3.81840.243569799441410.175502030942727X-RAY DIFFRACTION97.4847042828
3.8184-4.80860.2085122215751370.1686766837522676X-RAY DIFFRACTION96.1709401709
4.8086-34.160.2119014151771470.1914015852712716X-RAY DIFFRACTION97.8134608814

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