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

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Basic information

Entry
Database: PDB / ID: 8dqq
TitleCrystal structure of Arabidopsis thaliana COSY in complex with scopoletin
ComponentsCoumarin Synthase
KeywordsPLANT PROTEIN / Coumarin Synthase / Trans/Cis Isomerase / BAHD Acyltransferase
Function / homology
Function and homology information


paclitaxel biosynthetic process / coumarin biosynthetic process / transferase activity / metal ion binding
Similarity search - Function
: / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
7-hydroxy-2H-chromen-2-one / ACETATE ION / Anthranilate N-hydroxycinnamoyl/benzoyltransferase, putative
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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)99,7666
Polymers99,4652
Non-polymers3014
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.907, 58.771, 273.611
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

#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
#2: Chemical ChemComp-07L / 7-hydroxy-2H-chromen-2-one / 7-hydroxycoumarin


Mass: 162.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O3 / 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-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
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: 47.45 %
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 umbelliferone, 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: 2.33→136.81 Å / Num. obs: 40091 / % possible obs: 97.43 % / Redundancy: 1.9 % / Biso Wilson estimate: 48.47 Å2 / CC1/2: 0.991 / Net I/σ(I): 9.4
Reflection shellResolution: 2.33→2.413 Å / Rmerge(I) obs: 0.7117 / Mean I/σ(I) obs: 1 / Num. unique obs: 7339 / CC1/2: 0.441 / CC star: 0.782 / Rpim(I) all: 0.7117 / Rrim(I) all: 1 / % possible all: 92.2

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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: 2.33→136.81 Å / SU ML: 0.3272 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.8537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3117 1935 4.84 %
Rwork0.2527 38064 -
obs0.2556 39999 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.89 Å2
Refinement stepCycle: LAST / Resolution: 2.33→136.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 18 110 6839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036919
X-RAY DIFFRACTIONf_angle_d0.67869395
X-RAY DIFFRACTIONf_chiral_restr0.04331027
X-RAY DIFFRACTIONf_plane_restr0.00561219
X-RAY DIFFRACTIONf_dihedral_angle_d15.83162497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.390.37621480.3092440X-RAY DIFFRACTION91.06
2.39-2.450.32441330.30782660X-RAY DIFFRACTION95.88
2.45-2.530.39441230.30542719X-RAY DIFFRACTION98.54
2.53-2.610.46141410.3122694X-RAY DIFFRACTION99.26
2.61-2.70.36391440.30382741X-RAY DIFFRACTION99.38
2.7-2.810.37781430.29052729X-RAY DIFFRACTION98.93
2.81-2.940.33961550.31052706X-RAY DIFFRACTION98.42
2.94-3.090.39211360.32062725X-RAY DIFFRACTION98.08
3.09-3.280.40511260.33022721X-RAY DIFFRACTION97.77
3.28-3.540.38111480.28052726X-RAY DIFFRACTION98.9
3.54-3.890.29951360.24282781X-RAY DIFFRACTION98.35
3.89-4.460.2771500.22092758X-RAY DIFFRACTION98.08
4.46-5.610.23961120.20452819X-RAY DIFFRACTION97.77
5.62-136.810.23541400.20842845X-RAY DIFFRACTION93.81

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