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- PDB-6ap8: Crystal Structure of rice D14 bound to 2-(2-methyl-3-nitroanilino... -

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Basic information

Entry
Database: PDB / ID: 6ap8
TitleCrystal Structure of rice D14 bound to 2-(2-methyl-3-nitroanilino)benzoic acid
ComponentsStrigolactone esterase D14
KeywordsPLANT PROTEIN / alpha/beta hydrolase
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
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-[(2-methyl-3-nitrophenyl)amino]benzoic acid / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.27 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: Strigolactone esterase D14
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4626
Polymers58,7332
Non-polymers7294
Water11,656647
1
A: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7313
Polymers29,3671
Non-polymers3642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7313
Polymers29,3671
Non-polymers3642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.005, 88.433, 119.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 53 - 317 / Label seq-ID: 4 - 268

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsMonomer as determined by gel filtration

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Components

#1: Protein Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2


Mass: 29366.695 Da / Num. of mol.: 2 / Fragment: residues 52-318
Source method: isolated from a genetically manipulated source
Details: gene was codon optimized for E.coli expression
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami 2
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-BNY / 2-[(2-methyl-3-nitrophenyl)amino]benzoic acid


Mass: 272.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.16 Å3/Da / Density % sol: 43.03 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES 0.1M, MPD 5%, PEG 6000 8%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.27→48.01 Å / Num. obs: 134179 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.042 / Rrim(I) all: 0.159 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.27-1.2914.31.99265690.5490.5432.066100
6.96-48.0113.10.049580.9980.0120.04299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.77 Å44.52 Å
Translation6.77 Å44.52 Å

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Processing

Software
NameVersionClassification
XDSdata processing
Aimless0.5.17data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W04

3w04


Resolution: 1.27→44.52 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.573 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.04
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1542 6862 5.1 %RANDOM
Rwork0.1192 ---
obs0.121 127214 100 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.57 Å2 / Biso mean: 13.154 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-0 Å2
2--0.68 Å20 Å2
3---0.67 Å2
Refinement stepCycle: final / Resolution: 1.27→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 52 647 4815
Biso mean--20.4 28.46 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194508
X-RAY DIFFRACTIONr_bond_other_d0.0120.024334
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.9646186
X-RAY DIFFRACTIONr_angle_other_deg1.76339907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.06421.872203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34815702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3871548
X-RAY DIFFRACTIONr_chiral_restr0.1360.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215273
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021147
X-RAY DIFFRACTIONr_rigid_bond_restr3.33138842
X-RAY DIFFRACTIONr_sphericity_free30.6545139
X-RAY DIFFRACTIONr_sphericity_bonded11.0859221
Refine LS restraints NCS

Ens-ID: 1 / Number: 31812 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.27→1.303 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 488 -
Rwork0.255 9294 -
all-9782 -
obs--100 %

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