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- PDB-6o5j: Crystal Structure of DAD2 bound to quinazolinone derivative -

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Basic information

Entry
Database: PDB / ID: 6o5j
TitleCrystal Structure of DAD2 bound to quinazolinone derivative
ComponentsProbable strigolactone esterase DAD2
KeywordsHORMONE / alpha/beta hydrolase
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-LM7 / DI(HYDROXYETHYL)ETHER / Probable strigolactone esterase DAD2
Similarity search - Component
Biological speciesPetunia hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsHamiaux, C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandPAF1301 New Zealand
Citation
Journal: Biochem.J. / Year: 2019
Title: Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode.
Authors: Hamiaux, C. / Larsen, L. / Lee, H.W. / Luo, Z. / Sharma, P. / Hawkins, B.C. / Perry, N.B. / Snowden, K.C.
#1: Journal: J. Biol. Chem. / Year: 2018
Title: Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: Structural and functional insights
Authors: Hamiaux, C. / Drummond, R.S.M. / Luo, Z. / Lee, H.W. / Sharma, P. / Janssen, B.J. / Perry, N.B. / Denny, W.A. / Snowden, K.C.
#2: Journal: Curr. Biol. / Year: 2012
Title: DAD2 is an a/b hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone
Authors: Hamiaux, C. / Drummond, R.S. / Janssen, B.J. / Ledger, S.E. / Cooney, J.M. / Newcomb, R.D. / Snowden, K.C.
History
DepositionMar 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable strigolactone esterase DAD2
B: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8018
Polymers58,8532
Non-polymers9486
Water9,260514
1
A: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8774
Polymers29,4271
Non-polymers4503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9244
Polymers29,4271
Non-polymers4973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.630, 56.830, 68.800
Angle α, β, γ (deg.)95.690, 94.590, 108.740
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 3 - 266 / Label seq-ID: 1 - 264

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable strigolactone esterase DAD2 / Protein DECREASED APICAL DOMINANCE 2


Mass: 29426.623 Da / Num. of mol.: 2 / Mutation: C89Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: DAD2 / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami 2
References: UniProt: J9U5U9, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 520 molecules

#2: Chemical ChemComp-LM7 / 1-(4-hydroxy-3-nitrophenyl)quinazoline-2,4(1H,3H)-dione


Mass: 299.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9N3O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.98 % / Mosaicity: 0.64 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1M Tris/Acetate, 0.2M MgCl2, 31% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.63→31.3 Å / Num. obs: 62194 / % possible obs: 96 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.63-1.663.90.60930330.7570.3540.70594.6
8.93-31.33.50.0353730.9960.0220.04293.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.26 Å29.35 Å
Translation5.26 Å29.35 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNP

4dnp


Resolution: 1.63→29.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.659 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1818 2954 5 %RANDOM
Rwork0.1438 ---
obs0.1457 56359 91.53 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 194.67 Å2 / Biso mean: 18.483 Å2 / Biso min: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.1 Å2-0.02 Å2
2---0.52 Å2-0.08 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.63→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 67 514 4735
Biso mean--23.12 29.13 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134445
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174085
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.6466070
X-RAY DIFFRACTIONr_angle_other_deg1.5941.5749401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.84120.782243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22215683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6131537
X-RAY DIFFRACTIONr_chiral_restr0.1130.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021031
Refine LS restraints NCS

Ens-ID: 1 / Number: 8761 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 131 -
Rwork0.203 2613 -
all-2744 -
obs--56.34 %
Refinement TLS params.

T11: 0.0087 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69980.09360.27290.63320.12471.1198-0.0008-0.0703-0.0111-0.0067-0.0244-0.01580.0039-0.02520.0252-0.03420.00570.1457-0.02990.022-18.27757.794-17.209
21.85750.2160.07340.86720.41641.2750.05610.1568-0.0267-0.00730.01860.0133-0.0324-0.0342-0.0747-0.02280.0040.1708-0.02960.0211-15.45476.39317.804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 266
2X-RAY DIFFRACTION2B3 - 266

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