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- PDB-6ap6: Crystal Structure of DAD2 in complex with tolfenamic acid -

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Basic information

Entry
Database: PDB / ID: 6ap6
TitleCrystal Structure of DAD2 in complex with tolfenamic acid
ComponentsProbable strigolactone esterase DAD2
KeywordsPLANT PROTEIN / 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
2-[(3-chloro-2-methylphenyl)amino]benzoic acid / Probable strigolactone esterase DAD2
Similarity search - Component
Biological speciesPetunia hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsHamiaux, C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
AGMARDT1323 New Zealand
MarsdenPAF1301 New Zealand
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Inhibition of strigolactone receptors byN-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.
#1: Journal: Curr. Biol. / Year: 2012
Title: DAD2 is an alpha/beta 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
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 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)60,2964
Polymers59,7722
Non-polymers5232
Water8,737485
1
A: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1482
Polymers29,8861
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1482
Polymers29,8861
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.860, 55.830, 69.230
Angle α, β, γ (deg.)95.760, 95.130, 108.460
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: 5 - 268

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

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Components

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


Mass: 29886.164 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
#2: Chemical ChemComp-TLF / 2-[(3-chloro-2-methylphenyl)amino]benzoic acid / Tolfenamic acid


Mass: 261.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12ClNO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.27 Å3/Da / Density % sol: 45.71 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris/Acetate 0.1M, MgCl2 0.2M, PEG 8000 24%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→34.67 Å / Num. obs: 56704 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.683.80.86827610.6480.5151.0189.8
9.04-34.673.70.0283160.9980.0170.03383.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.18 Å30.42 Å
Translation5.18 Å30.42 Å

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Processing

Software
NameVersionClassification
iMOSFLMdata processing
Aimless0.5.4data scaling
PHASER2.5.7phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNP

4dnp


Resolution: 1.65→30.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.764 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2868 5.1 %RANDOM
Rwork0.1681 ---
obs0.1697 53834 91.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 161.08 Å2 / Biso mean: 21.885 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0.33 Å20.15 Å2
2---0.97 Å2-0.18 Å2
3---0.92 Å2
Refinement stepCycle: final / Resolution: 1.65→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 36 485 4675
Biso mean--12 28.58 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194366
X-RAY DIFFRACTIONr_bond_other_d0.0060.024140
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9575951
X-RAY DIFFRACTIONr_angle_other_deg1.21239453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97622.549204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76315678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121538
X-RAY DIFFRACTIONr_chiral_restr0.0870.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215029
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021105
Refine LS restraints NCS

Ens-ID: 1 / Number: 32966 / 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: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 195 -
Rwork0.286 3969 -
all-4164 -
obs--89.99 %
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)
11.92680.19370.50210.69570.12271.4-0.0093-0.0850.0121-0.0126-0.0194-0.04930.0215-0.06350.02870.0047-0.02960.00870.2345-0.04690.025-16.4757.624-19.519
21.74240.24810.03960.99710.53361.36060.04730.1375-0.00420.04310.01490.0051-0.0409-0.0379-0.06220.0104-0.02390.00880.2563-0.05040.0191-13.52175.54615.522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 266
2X-RAY DIFFRACTION2B3 - 266

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