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- PDB-8th2: Structure of the isoflavene-forming dirigent protein PsPTS2 -

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Basic information

Entry
Database: PDB / ID: 8th2
TitleStructure of the isoflavene-forming dirigent protein PsPTS2
ComponentsDirigent protein
KeywordsPLANT PROTEIN / dirigent protein / isoflavene / lignan / pterocarpan / aromatic diterpenoids
Function / homologyDirigent protein / Dirigent-like protein / Allene oxide cyclase/Dirigent protein / phenylpropanoid biosynthetic process / apoplast / Dirigent protein
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSmith, C.A. / Meng, Q. / Lewis, N.G. / Davin, L.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG-0397ER20259 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea.
Authors: Meng, Q. / Moinuddin, S.G.A. / Celoy, R.M. / Smith, C.A. / Young, R.P. / Costa, M.A. / Freeman, R.A. / Fukaya, M. / Kim, D.N. / Cort, J.R. / Hawes, M.C. / van Etten, H.D. / Pandey, P. / ...Authors: Meng, Q. / Moinuddin, S.G.A. / Celoy, R.M. / Smith, C.A. / Young, R.P. / Costa, M.A. / Freeman, R.A. / Fukaya, M. / Kim, D.N. / Cort, J.R. / Hawes, M.C. / van Etten, H.D. / Pandey, P. / Chittiboyina, A.G. / Ferreira, D. / Davin, L.B. / Lewis, N.G.
History
DepositionJul 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dirigent protein
B: Dirigent protein
C: Dirigent protein
D: Dirigent protein
E: Dirigent protein
F: Dirigent protein


Theoretical massNumber of molelcules
Total (without water)145,4016
Polymers145,4016
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22870 Å2
ΔGint-150 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.138, 162.183, 232.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Dirigent protein


Mass: 24233.418 Da / Num. of mol.: 6 / Mutation: K179E,A204E,M214I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: KIW84_032295 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9D4XSX2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1.0 M ammonium tartrate dibasic, 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→90.4 Å / Num. obs: 39978 / % possible obs: 94.7 % / Redundancy: 5.4 % / CC1/2: 0.991 / Rpim(I) all: 0.127 / Rrim(I) all: 0.222 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1964 / CC1/2: 0.703 / Rpim(I) all: 0.604

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→90.4 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 1998 5.03 %
Rwork0.1963 --
obs0.1991 39685 69.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→90.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7683 0 0 87 7770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097892
X-RAY DIFFRACTIONf_angle_d1.20210702
X-RAY DIFFRACTIONf_dihedral_angle_d7.5691046
X-RAY DIFFRACTIONf_chiral_restr0.0651193
X-RAY DIFFRACTIONf_plane_restr0.0081373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.4017320.3138624X-RAY DIFFRACTION16
2.67-2.740.371340.2834787X-RAY DIFFRACTION20
2.74-2.820.3777500.2974981X-RAY DIFFRACTION26
2.82-2.910.3635770.29841389X-RAY DIFFRACTION36
2.91-3.010.34821090.29211894X-RAY DIFFRACTION49
3.01-3.130.28311140.2752401X-RAY DIFFRACTION62
3.13-3.280.28831530.25042910X-RAY DIFFRACTION75
3.28-3.450.33581690.23413456X-RAY DIFFRACTION89
3.45-3.660.26652070.21233672X-RAY DIFFRACTION95
3.66-3.950.26492050.18993865X-RAY DIFFRACTION99
3.95-4.340.22471910.15863875X-RAY DIFFRACTION100
4.34-4.970.18172160.13543881X-RAY DIFFRACTION99
4.97-6.270.23272220.16763929X-RAY DIFFRACTION100
6.27-90.40.23012190.19914023X-RAY DIFFRACTION98

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