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- PDB-7sgy: Cannabis sativa bibenzyl synthase -

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Basic information

Entry
Database: PDB / ID: 7sgy
TitleCannabis sativa bibenzyl synthase
ComponentsBibenzyl synthase
KeywordsLIGASE / Type III polypeptide synthase
Function / homologyChalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase-like / Uncharacterized protein
Function and homology information
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKimber, M.S. / Forrester, T.J.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)2020-07113 Canada
CitationJournal: Plant J. / Year: 2022
Title: Bibenzyl synthesis in Cannabis sativa L.
Authors: Boddington, K.F. / Soubeyrand, E. / Van Gelder, K. / Casaretto, J.A. / Perrin, C. / Forrester, T.J.B. / Parry, C. / Al-Abdul-Wahid, M.S. / Jentsch, N.G. / Magolan, J. / Bozzo, G.G. / Kimber, ...Authors: Boddington, K.F. / Soubeyrand, E. / Van Gelder, K. / Casaretto, J.A. / Perrin, C. / Forrester, T.J.B. / Parry, C. / Al-Abdul-Wahid, M.S. / Jentsch, N.G. / Magolan, J. / Bozzo, G.G. / Kimber, M.S. / Rothstein, S.J. / Akhtar, T.A.
History
DepositionOct 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bibenzyl synthase
B: Bibenzyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9504
Polymers93,8792
Non-polymers712
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-33 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.440, 59.580, 70.940
Angle α, β, γ (deg.)90.000, 107.698, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Bibenzyl synthase


Mass: 46939.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pET28a tag at N-terminus / Source: (gene. exp.) Cannabis sativa (plant) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A803NJB5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.49 Å3/Da / Density % sol: 17.4 % / Description: prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 5 mg/ml protein, 0.15 M potassium bromide, 30 % polyethylene glycol mono-methyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.5→44.69 Å / Num. obs: 19257 / % possible obs: 99.6 % / Redundancy: 3.36 % / Biso Wilson estimate: 46.46 Å2 / CC1/2: 0.997 / Rsym value: 0.084 / Net I/σ(I): 9.23
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2127 / CC1/2: 0.818 / Rrim(I) all: 0.587 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DXB

6dxb


Resolution: 2.5→44.69 Å / SU ML: 0.2968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.44
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2277 960 4.99 %
Rwork0.1845 18280 -
obs0.1867 19240 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5983 0 2 121 6106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196118
X-RAY DIFFRACTIONf_angle_d0.45968269
X-RAY DIFFRACTIONf_chiral_restr0.0393919
X-RAY DIFFRACTIONf_plane_restr0.00311067
X-RAY DIFFRACTIONf_dihedral_angle_d19.50742271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.31221340.25912577X-RAY DIFFRACTION99.6
2.63-2.80.32651360.25022604X-RAY DIFFRACTION99.67
2.8-3.010.3261370.22512593X-RAY DIFFRACTION99.64
3.01-3.320.24251360.19992608X-RAY DIFFRACTION99.6
3.32-3.790.24831370.16942602X-RAY DIFFRACTION99.71
3.8-4.780.15521380.15432607X-RAY DIFFRACTION99.17
4.78-44.690.2081420.17152689X-RAY DIFFRACTION99.72
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)
11.86441013348-0.1446106613220.1941020556154.59379742801-1.869785007322.866451978450.00183688183613-0.330996171824-0.435087491874-0.4212906688610.1267426083720.101614448220.418766804158-0.155400416684-0.1302655340640.261468557104-0.01351832890720.0455196170770.401395791994-0.01241627017290.3475305416220.07123158658716.2475537721929.4241250533
23.258653657860.676021350247-0.4950276242522.59276135464-0.6786915302424.833238547290.103578937629-0.193718477596-0.113801729364-0.109741283359-0.139633496886-0.0496694810970.03959391283510.2794504655940.04062122828850.203605341560.01851756428110.03972867800330.256986344622-0.03657523170030.2154516594964.1658447387418.925278296723.4957977279
31.11373005444-0.8392350524760.007053254703795.800541896371.942516182885.75945832751-0.165961684387-0.1274165972160.02360989138430.1776086311150.105848245288-0.9687510934450.2094590966311.49877403294-0.008024720176740.426038857757-0.07294564131370.00807354062190.8725214928120.1520056814970.47714291771516.614450349714.96036628139.1266901907
43.075328199550.4856098963931.095427739284.83341778899-0.5484196902444.19753914547-0.0776693756923-0.4238149739550.1741269053890.486961477783-0.01519117089320.456701557737-0.402236622750.1034738009270.1644715907450.440642934305-0.02497448386130.07175888347780.446585701346-0.05548342855640.2363570531023.5214396220423.545820913639.2201224813
51.329204808490.8621233454420.1494335402192.643735904080.9607652590133.24227526051-0.1338343997190.0134875263921-0.377258459603-0.115042616130.182486905539-0.1986606342330.5427658152850.845920478525-0.1359278563340.5287097192210.115727603140.1315174658740.8703675741990.07939709620920.45339575542423.54502030016.935012307034.08085734733
61.92811082568-0.710382372843-0.5594322525452.215136503410.0866377969783.789117887590.120597438856-0.174154734586-0.07487247594850.0725373511681-0.187517973739-0.211151305124-0.007530624175190.6844045488230.09022298782430.295770923093-0.02331312975390.0529031097330.6026842458620.06844672437030.26239189067420.197036772919.080612702711.8811777739
71.009460646261.09898886863-0.842409293182.44946212037-2.270899299595.41676105538-0.01468249923410.244572258975-0.0127066063244-0.812550356897-0.02936687331250.05209331014450.414576021214-0.4286480962910.03451423240540.4509248434750.060742024570.04532525422110.462387224751-0.04920516123550.3116783412987.2026283467219.7759749112-3.65646931906
81.72517391038-0.439312229575-0.4944563977762.523875038580.7368331562893.243465331370.02355623322630.05357845667770.113431055199-0.582723550655-0.0171349777126-0.507881017257-0.1919175569440.807515203282-0.04166568186950.464211857875-0.008336288870280.1046787729180.5565667202880.03586544675130.29975793139820.840629698725.7754962225-3.10821678114
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 119 )AA5 - 1191 - 116
22chain 'A' and (resid 120 through 249 )AA120 - 249117 - 246
33chain 'A' and (resid 250 through 323 )AA250 - 323247 - 314
44chain 'A' and (resid 324 through 393 )AA324 - 393315 - 384
55chain 'B' and (resid 6 through 119 )BB6 - 1191 - 114
66chain 'B' and (resid 120 through 249 )BB120 - 249115 - 244
77chain 'B' and (resid 250 through 323 )BB250 - 323245 - 318
88chain 'B' and (resid 324 through 392 )BB324 - 392319 - 387

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