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- PDB-8dqo: Crystal structure of Arabidopsis thaliana COSY -

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Basic information

Entry
Database: PDB / ID: 8dqo
TitleCrystal structure of Arabidopsis thaliana COSY
ComponentsCoumarin Synthase
KeywordsPLANT PROTEIN / Coumarin Synthase
Function / homology: / paclitaxel biosynthetic process / coumarin biosynthetic process / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / transferase activity / metal ion binding / Anthranilate N-hydroxycinnamoyl/benzoyltransferase, putative
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)100,22715
Polymers99,4652
Non-polymers76313
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.411, 57.903, 270.395
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: 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-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.56 %
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
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: 1.9→48.72 Å / Num. obs: 71357 / % possible obs: 98.65 % / Redundancy: 1.1 % / CC1/2: 1 / Net I/σ(I): 13.42
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 1.1 % / Num. unique obs: 6352 / CC1/2: 1 / % possible all: 89.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0B

4g0b


Resolution: 1.9→48.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.689 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23017 3653 5.1 %RANDOM
Rwork0.1896 ---
obs0.1916 67704 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.26 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 46 351 7203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0147038
X-RAY DIFFRACTIONr_bond_other_d0.0040.0176299
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.659530
X-RAY DIFFRACTIONr_angle_other_deg0.9511.64414756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17522.401354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.345151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8351540
X-RAY DIFFRACTIONr_chiral_restr0.0660.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021340
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_it0.8841.5833501
X-RAY DIFFRACTIONr_mcbond_other0.8841.5833500
X-RAY DIFFRACTIONr_mcangle_it1.52.3664371
X-RAY DIFFRACTIONr_mcangle_other1.52.3664372
X-RAY DIFFRACTIONr_scbond_it1.0911.7243537
X-RAY DIFFRACTIONr_scbond_other1.0881.7233537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7422.5215160
X-RAY DIFFRACTIONr_long_range_B_refined4.89218.8117758
X-RAY DIFFRACTIONr_long_range_B_other4.89218.8187759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å
RfactorNum. reflection% reflection
Rfree0.27 259 -
Rwork0.235 4203 -
obs--84.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.992-0.5142-0.34420.96730.37990.7268-0.0115-0.17550.04880.08810.0232-0.0734-0.05270.0495-0.01170.0927-0.0226-0.01960.0620.00130.008324.53034.826614.4061
21.45370.1191.0181.10970.14192.0807-0.0347-0.08060.06250.03860.03530.18560.0415-0.2337-0.00060.26170.0026-0.02930.22470.02480.039712.6049-4.071449.5798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 451
2X-RAY DIFFRACTION2B2 - 451

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