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- PDB-8dqp: Crystal structure of Arabidopsis thaliana COSY in complex with sc... -

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Basic information

Entry
Database: PDB / ID: 8dqp
TitleCrystal structure of Arabidopsis thaliana COSY in complex with scopoletin
ComponentsCoumarin Synthase
KeywordsPLANT PROTEIN / Coumarin Synthase / Trans/Cis Isomerase / BAHD Acyltransferase
Function / homologycoumarin biosynthetic process / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / transferase activity / ACETATE ION / 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one / Anthranilate N-hydroxycinnamoyl/benzoyltransferase, putative
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKim, C.Y. / Mitchell, A.J. / Gutierrez, M. / Weng, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
W. M. Keck Foundation United States
Other privateFamily Larsson-Rosenquist Foundation
Other privateBeckman Young Investigator Program
CitationJournal: Nat Commun / Year: 2023
Title: Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY.
Authors: Kim, C.Y. / Mitchell, A.J. / Kastner, D.W. / Albright, C.E. / Gutierrez, M.A. / Glinkerman, C.M. / Kulik, H.J. / Weng, J.K.
History
DepositionJul 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coumarin Synthase
B: Coumarin Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1149
Polymers99,4652
Non-polymers6507
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.459, 58.349, 273.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Coumarin Synthase / HXXXD-type acyl-transferase family protein / Anthranilate N-hydroxycinnamoyl/benzoyltransferase / putative


Mass: 49732.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g28680, F1K23.12, F1K23_12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8LF28

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Non-polymers , 6 types, 129 molecules

#2: Chemical ChemComp-T83 / 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one / Scopoletin


Mass: 192.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM calcium acetate, 0.1M sodium cacodylate pH 6.5, 20% glycerol, 500 uM scopoletin, 5 mg/mL protein
PH range: 6.5-7.5 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.48→136.09 Å / Num. obs: 33466 / % possible obs: 97.46 % / Redundancy: 1.9 % / Biso Wilson estimate: 60.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.64
Reflection shellResolution: 2.48→2.569 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7324 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 3278 / CC1/2: 0.474 / CC star: 0.802 / Rpim(I) all: 0.7324 / Rrim(I) all: 1.036 / % possible all: 96.88

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DQO

8dqo


Resolution: 2.48→68.32 Å / SU ML: 0.3893 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 36.6216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2808 1550 4.65 %
Rwork0.173 31802 -
obs0.1781 33352 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→68.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 41 122 6712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02366754
X-RAY DIFFRACTIONf_angle_d2.36799149
X-RAY DIFFRACTIONf_chiral_restr0.1054991
X-RAY DIFFRACTIONf_plane_restr0.02321184
X-RAY DIFFRACTIONf_dihedral_angle_d17.29692457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.560.38041340.2962838X-RAY DIFFRACTION96.68
2.56-2.650.37121650.25652847X-RAY DIFFRACTION98.85
2.65-2.760.29871370.22242891X-RAY DIFFRACTION99.12
2.76-2.880.35051490.21322817X-RAY DIFFRACTION97.73
2.88-3.040.39491250.18182923X-RAY DIFFRACTION98.83
3.04-3.230.3421640.18722862X-RAY DIFFRACTION98.41
3.23-3.470.28251340.16972860X-RAY DIFFRACTION96.99
3.47-3.820.26821070.15312957X-RAY DIFFRACTION98.58
3.82-4.380.28161350.14592932X-RAY DIFFRACTION97.83
4.38-5.510.23281480.14252883X-RAY DIFFRACTION95.74
5.52-68.320.2511520.1842992X-RAY DIFFRACTION93.85

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