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- PDB-6ooc: Structure of the pterocarpan synthase dirigent protein GePTS1 -

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Basic information

Entry
Database: PDB / ID: 6ooc
TitleStructure of the pterocarpan synthase dirigent protein GePTS1
ComponentsDirigent protein
KeywordsPLANT PROTEIN / Dirigent protein / apo-form
Function / homologypterocarpan synthase / pterocarpan synthase activity / Dirigent protein / Dirigent-like protein / Allene oxide cyclase/Dirigent protein / phenylpropanoid biosynthetic process / apoplast / defense response / Pterocarpan synthase 1
Function and homology information
Biological speciesGlycyrrhiza echinata (hedgehog licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.2Oct 11, 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: Dirigent protein
B: Dirigent protein
C: Dirigent protein
D: Dirigent protein
E: Dirigent protein
F: Dirigent protein


Theoretical massNumber of molelcules
Total (without water)145,5896
Polymers145,5896
Non-polymers00
Water1,820101
1
A: Dirigent protein
B: Dirigent protein
C: Dirigent protein


Theoretical massNumber of molelcules
Total (without water)72,7953
Polymers72,7953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-55 kcal/mol
Surface area19900 Å2
MethodPISA
2
D: Dirigent protein
E: Dirigent protein
F: Dirigent protein


Theoretical massNumber of molelcules
Total (without water)72,7953
Polymers72,7953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-49 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.572, 162.572, 99.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Dirigent protein


Mass: 24264.834 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycyrrhiza echinata (hedgehog licorice)
Gene: PTS1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V1FH01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M sodium phosphate-monobasic, 0.18 M sodium citrate pH 4.2, 9% PEG 20000 (w/v)

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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: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→39.1 Å / Num. obs: 46983 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rpim(I) all: 0.037 / Rrim(I) all: 0.125 / Net I/σ(I): 13.1
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 4596 / CC1/2: 0.598 / Rpim(I) all: 0.526 / Rrim(I) all: 1.821

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LAL

5lal


Resolution: 2.6→39.049 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 2331 4.96 %
Rwork0.1968 44620 -
obs0.1989 46951 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.39 Å2 / Biso mean: 66.9012 Å2 / Biso min: 45.94 Å2
Refinement stepCycle: final / Resolution: 2.6→39.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 0 101 7903
Biso mean---60.51 -
Num. residues----1009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.65310.32191400.278226012741
2.6531-2.71080.32251640.276725822746
2.7108-2.77380.33191350.277825802715
2.7738-2.84320.41571360.284525932729
2.8432-2.920.31961280.288725972725
2.92-3.00590.31021350.263126242759
3.0059-3.10290.3441450.243225962741
3.1029-3.21370.30661330.224226152748
3.2137-3.34240.25671450.230426142759
3.3424-3.49440.30211300.227425762706
3.4944-3.67850.24731250.205326582783
3.6785-3.90870.23411320.191126262758
3.9087-4.21020.23571070.178926612768
4.2102-4.63330.17741580.136626082766
4.6333-5.30230.17591550.152526372792
5.3023-6.6750.21481180.182126952813
6.675-39.05290.21551450.19427572902

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