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

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Basic information

Entry
Database: PDB / ID: 8dqr
TitleCrystal structure of Arabidopsis thaliana COSY in complex with scopoletin
ComponentsCoumarin Synthase
KeywordsPLANT PROTEIN / Coumarin Synthase / Trans/Cis Isomerase / BAHD Acyltransferase
Function / homology: / coumarin biosynthetic process / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / transferase activity / metal ion binding / COENZYME A / Anthranilate N-hydroxycinnamoyl/benzoyltransferase, putative
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coumarin Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6484
Polymers49,7481
Non-polymers9003
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.514, 88.886, 96.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 49748.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C308 is modeled as a CSO (sulfenic acid) / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g28680, F1K23.12, F1K23_12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8LF28
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM calcium acetate, 0.1 M sodium cacodylate pH 6.5, 20% glycerol, 500 uM coenzyme-A, 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-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.26→65.5 Å / Num. obs: 23643 / % possible obs: 97.02 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 12.69
Reflection shellResolution: 2.26→2.341 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7622 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 2179 / CC1/2: 0.425 / CC star: 0.772 / Rpim(I) all: 0.7622 / % possible all: 90.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DQO

8dqo


Resolution: 2.26→65.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.911 / SU B: 32.377 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29135 1189 5 %RANDOM
Rwork0.19122 ---
obs0.19636 22455 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.561 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2---2.67 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.26→65.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 55 143 3583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0143528
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173134
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6714795
X-RAY DIFFRACTIONr_angle_other_deg0.9071.6487346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6915432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18922.386176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70915565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.861520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02671
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6123.6851731
X-RAY DIFFRACTIONr_mcbond_other3.5943.6841730
X-RAY DIFFRACTIONr_mcangle_it4.8065.5232159
X-RAY DIFFRACTIONr_mcangle_other4.815.5232160
X-RAY DIFFRACTIONr_scbond_it3.7923.9391797
X-RAY DIFFRACTIONr_scbond_other3.793.9391797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7445.812636
X-RAY DIFFRACTIONr_long_range_B_refined5.64444.0763894
X-RAY DIFFRACTIONr_long_range_B_other5.62943.9983885
X-RAY DIFFRACTIONr_rigid_bond_restr1.8636662
X-RAY DIFFRACTIONr_sphericity_free37.952569
X-RAY DIFFRACTIONr_sphericity_bonded18.21356651
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 75 -
Rwork0.463 1569 -
obs--93.3 %
Refinement TLS params.Method: refined / Origin x: 13.3768 Å / Origin y: 0.435 Å / Origin z: -10.5132 Å
111213212223313233
T0.0159 Å2-0.0235 Å2-0.0008 Å2-0.2338 Å2-0.0057 Å2--0.0653 Å2
L0.2684 °2-0.4417 °2-0.3577 °2-2.309 °20.777 °2--0.9652 °2
S-0.0324 Å °0.0381 Å °-0.1038 Å °-0.0433 Å °0.0012 Å °0.1844 Å °0.0825 Å °-0.0634 Å °0.0312 Å °

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