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- PDB-6ood: Structure of the pterocarpan synthase dirigent protein PsPTS1 -

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Entry
Database: PDB / ID: 6ood
TitleStructure of the pterocarpan synthase dirigent protein PsPTS1
Componentspterocarpan synthase dirigent protein PsPTS1
KeywordsPLANT PROTEIN / Dirigent protein / apo-form
Function / homologyAOC barrel-like / Allene oxide cyclase-like / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSmith, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG-0397ER20259 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains.
Authors: Meng, Q. / Moinuddin, S.G.A. / Kim, S.J. / Bedgar, D.L. / Costa, M.A. / Thomas, D.G. / Young, R.P. / Smith, C.A. / Cort, J.R. / Davin, L.B. / Lewis, N.G.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: pterocarpan synthase dirigent protein PsPTS1


Theoretical massNumber of molelcules
Total (without water)22,1331
Polymers22,1331
Non-polymers00
Water3,315184
1
A: pterocarpan synthase dirigent protein PsPTS1

A: pterocarpan synthase dirigent protein PsPTS1

A: pterocarpan synthase dirigent protein PsPTS1


Theoretical massNumber of molelcules
Total (without water)66,4003
Polymers66,4003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6430 Å2
ΔGint-38 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.893, 78.893, 78.893
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-484-

HOH

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Components

#1: Protein pterocarpan synthase dirigent protein PsPTS1


Mass: 22133.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.85 Å3/Da / Density % sol: 33.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 0.25 M sodium acetate trihydrate, pH 4.9, 10 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.48→35.3 Å / Num. obs: 27529 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.073 / Net I/σ(I): 14.6
Reflection shellResolution: 1.48→1.51 Å / Num. unique obs: 1369 / CC1/2: 0.72 / Rpim(I) all: 0.387 / Rrim(I) all: 1.065

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→35.282 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.96
RfactorNum. reflection% reflection
Rfree0.1907 1315 5.02 %
Rwork0.1624 --
obs0.1638 26219 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.7 Å2 / Biso mean: 22.2996 Å2 / Biso min: 10.2 Å2
Refinement stepCycle: final / Resolution: 1.5→35.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 0 186 1390
Biso mean---33.37 -
Num. residues----155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.56010.2091650.166527552920100
1.5601-1.63110.20971460.158427522898100
1.6311-1.71710.22361450.144627742919100
1.7171-1.82470.19231510.136927522903100
1.8247-1.96560.26171360.23072615275194
1.9656-2.16340.20521300.147427902920100
2.1634-2.47630.24071430.19812729287297
2.4763-3.11960.21530.16328162969100
3.1196-35.29180.13691460.143529213067100

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