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- PDB-6mk2: Crystal structure of Coleus blumei rosmarinic acid synthase (RAS)... -

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Basic information

Entry
Database: PDB / ID: 6mk2
TitleCrystal structure of Coleus blumei rosmarinic acid synthase (RAS) in complex with 4-coumaroyl-(R)-3-(4-hydroxyphenyl)lactate
ComponentsRosmarinate synthase
KeywordsTRANSFERASE / BAHD acyltransferase / hydroxycinnamoyltransferase
Function / homology
Function and homology information


rosmarinate synthase / rosmarinate synthase activity
Similarity search - Function
: / Transferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JUV / Rosmarinate synthase
Similarity search - Component
Biological speciesPlectranthus scutellarioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsWeng, J.K. / Levsh, O.L.
Funding support United States, 3items
OrganizationGrant numberCountry
Other privatePew Charitable Trust 27345 United States
Howard Hughes Medical Institute (HHMI) United States
Other privateSearle Scholars Program 15-SSP-162 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants.
Authors: Levsh, O. / Pluskal, T. / Carballo, V. / Mitchell, A.J. / Weng, J.K.
History
DepositionSep 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Rosmarinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2862
Polymers47,9581
Non-polymers3281
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.900, 76.320, 68.050
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rosmarinate synthase / CbRAS / Hydroxycinnamoyl transferase / CbHCT1


Mass: 47958.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plectranthus scutellarioides (plant) / Gene: RAS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PDV5, rosmarinate synthase
#2: Chemical ChemComp-JUV / (2R)-3-(4-hydroxyphenyl)-2-{[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]oxy}propanoic acid / 4-coumaroyl-(R)-3-(4-hydroxyphenyl)lactate


Mass: 328.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16O6

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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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 microliters of 10 mg/mL protein was mixed with 1 microliter of a reservoir solution containing 0.2 M magnesium chloride, 0.1 M sodium TAPS (pH 8.5), 21% PEG 8000, and 15 mM 4-coumaroyl-(R)- ...Details: 2 microliters of 10 mg/mL protein was mixed with 1 microliter of a reservoir solution containing 0.2 M magnesium chloride, 0.1 M sodium TAPS (pH 8.5), 21% PEG 8000, and 15 mM 4-coumaroyl-(R)-3-(4-hydroxyphenyl)lactate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.35→45.28 Å / Num. obs: 6696 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.982 / Rmerge(I) obs: 0.143 / Net I/σ(I): 7
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.561 / Num. unique obs: 978 / CC1/2: 0.565 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→45.277 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 34.31
RfactorNum. reflection% reflection
Rfree0.3286 1256 9.88 %
Rwork0.2769 --
obs0.2819 12718 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.35→45.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 24 0 3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073319
X-RAY DIFFRACTIONf_angle_d1.3514518
X-RAY DIFFRACTIONf_dihedral_angle_d5.1121954
X-RAY DIFFRACTIONf_chiral_restr0.048476
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3501-3.48420.43021470.3471321X-RAY DIFFRACTION98
3.4842-3.64270.33261430.30651258X-RAY DIFFRACTION97
3.6427-3.83460.3831420.32581245X-RAY DIFFRACTION98
3.8346-4.07470.37651330.29891257X-RAY DIFFRACTION97
4.0747-4.38910.30331380.27881278X-RAY DIFFRACTION98
4.3891-4.83030.34091270.27091279X-RAY DIFFRACTION97
4.8303-5.52820.27111420.26881228X-RAY DIFFRACTION96
5.5282-6.96090.35211430.28481299X-RAY DIFFRACTION99
6.9609-45.28130.28361410.22711297X-RAY DIFFRACTION100

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