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- PDB-4dnp: Crystal Structure of DAD2 -

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Basic information

Entry
Database: PDB / ID: 4dnp
TitleCrystal Structure of DAD2
ComponentsDAD2
KeywordsHYDROLASE / 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
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Probable strigolactone esterase DAD2
Similarity search - Component
Biological speciesPetunia hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsHamiaux, C.
CitationJournal: 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
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1083
Polymers29,8611
Non-polymers2462
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DAD2
hetero molecules

A: DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2156
Polymers59,7222
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.260, 129.260, 129.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
DetailsThis protein behaves as a monomer on gel filtration column

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Components

#1: Protein DAD2


Mass: 29861.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: gene was codon optimized for E.coli expression / 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*PLUS
#2: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.1
Details: (NH4)2HPO4 0.6M, pH 7.1, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979417 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979417 Å / Relative weight: 1
ReflectionResolution: 2.15→40.876 Å / Num. all: 19684 / Num. obs: 19684 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.2722.10.4587.76282828480.458100
2.27-2.4220.3529.75920426920.352100
2.4-2.57220.26512.35545625210.265100
2.57-2.7821.90.215.55182623670.2100
2.78-3.0421.80.14220.84750921810.142100
3.04-3.421.60.11527.24337020050.115100
3.4-3.9321.30.09832.93691717320.098100
3.93-4.81200.07736.63000214970.077100
4.81-6.821.90.0835.42566611700.08100
6.8-40.876210.05640.4141216710.05699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.08 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.88 Å
Translation2.5 Å40.88 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40.876 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2082 / WRfactor Rwork: 0.1658 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8912 / SU B: 8.332 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1778 / SU Rfree: 0.1607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1006 5.1 %RANDOM
Rwork0.167 18665 --
obs0.1692 19671 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.69 Å2 / Biso mean: 26.5934 Å2 / Biso min: 8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.161 Å0.178 Å
Refinement stepCycle: LAST / Resolution: 2.15→40.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 14 182 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222137
X-RAY DIFFRACTIONr_bond_other_d0.0010.021440
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9552904
X-RAY DIFFRACTIONr_angle_other_deg0.9613.0013474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14722.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76215332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0051519
X-RAY DIFFRACTIONr_chiral_restr0.1070.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_mcbond_it0.7661.51310
X-RAY DIFFRACTIONr_mcbond_other0.2071.5533
X-RAY DIFFRACTIONr_mcangle_it1.47122111
X-RAY DIFFRACTIONr_scbond_it2.53827
X-RAY DIFFRACTIONr_scangle_it4.054.5792
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 79 -
Rwork0.175 1372 -
all-1451 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -44.594 Å / Origin y: -43.472 Å / Origin z: 8.513 Å
111213212223313233
T0.1078 Å20.0304 Å2-0.0818 Å2-0.0499 Å20.001 Å2--0.0911 Å2
L3.0324 °2-0.395 °20.278 °2-1.4501 °2-0.1872 °2--1.2537 °2
S-0.153 Å °-0.2391 Å °0.1327 Å °0.0647 Å °0.0455 Å °-0.0938 Å °-0.1377 Å °0.021 Å °0.1076 Å °

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