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- PDB-6uh8: Crystal structure of DAD2 N242I mutant -

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Basic information

Entry
Database: PDB / ID: 6uh8
TitleCrystal structure of DAD2 N242I mutant
ComponentsDecreased Apical Dominance 2
KeywordsHYDROLASE / Strigolactone receptor
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds / hydrolase activity
Similarity search - Function
Strigolactone esterase D14 family / 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
Probable strigolactone esterase DAD2 / DAD2
Similarity search - Component
Biological speciesPetunia hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsSharma, P. / Hamiaux, C. / Snowden, K.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandPAF1301 New Zealand
Citation
Journal: J.Biol.Chem. / Year: 2020
Title: Flexibility of the petunia strigolactone receptor DAD2 promotes its interaction with signaling partners.
Authors: Lee, H.W. / Sharma, P. / Janssen, B.J. / Drummond, R.S.M. / Luo, Z. / Hamiaux, C. / Collier, T. / Allison, J.R. / Newcomb, R.D. / 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
DepositionSep 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: 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 1.2Apr 8, 2020Group: 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 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Decreased Apical Dominance 2
B: Decreased Apical Dominance 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,80316
Polymers59,7702
Non-polymers1,03314
Water7,927440
1
A: Decreased Apical Dominance 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1974
Polymers29,8851
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decreased Apical Dominance 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,60712
Polymers29,8851
Non-polymers72111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-64 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.736, 133.736, 99.764
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 2 - 265 / Label seq-ID: 4 - 267

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 Decreased Apical Dominance 2 / DAD2


Mass: 29885.219 Da / Num. of mol.: 2 / Mutation: N242I, C89Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: dad2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami 2 / References: UniProt: L7MTK5, UniProt: J9U5U9*PLUS

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Non-polymers , 5 types, 454 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5 1.58-1.72 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953736 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953736 Å / Relative weight: 1
ReflectionResolution: 1.58→45.86 Å / Num. obs: 138411 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.021 / Rrim(I) all: 0.09 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.58-1.6118.92.18812877968180.7280.5172.2481.6100
8.65-45.81180.0351603989110.0090.03672.299.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.75 Å45.81 Å
Translation6.75 Å45.81 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.31data scaling
PHASER2.7.17phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNP

4dnp


Resolution: 1.58→45.81 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.854 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1649 9970 7.2 %RANDOM
Rwork0.138 ---
obs0.1399 128380 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.15 Å2 / Biso mean: 26.861 Å2 / Biso min: 15.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20.74 Å20 Å2
2--1.48 Å2-0 Å2
3----4.81 Å2
Refinement stepCycle: final / Resolution: 1.58→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 58 440 4640
Biso mean--41.07 42.02 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134459
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174144
X-RAY DIFFRACTIONr_angle_refined_deg1.741.6296085
X-RAY DIFFRACTIONr_angle_other_deg1.5691.579544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.71120.324247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97415696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.061541
X-RAY DIFFRACTIONr_chiral_restr0.1020.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
X-RAY DIFFRACTIONr_rigid_bond_restr3.78238603
X-RAY DIFFRACTIONr_sphericity_free41.6385313
X-RAY DIFFRACTIONr_sphericity_bonded25.25758623
Refine LS restraints NCS

Ens-ID: 1 / Number: 8537 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 709 -
Rwork0.274 9482 -
all-10191 -
obs--100 %
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)
10.00070.0047-0.0010.0341-0.00760.00170.000900.00070.0019-0.00030.0077-0.00030.0001-0.00070.0030.0004-00.00070.00010.087337.6053.173-4.278
20.0545-0.00650.00960.01470.00720.0129-00.00720.00480-0.00140.00110.00010.00060.00140-00.00030.0010.00080.08253.19335.66-10.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 265
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B2 - 265
4X-RAY DIFFRACTION2B301

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