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- PDB-3adg: Structure of Arabidopsis HYL1 and its molecular implications for ... -

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Basic information

Entry
Database: PDB / ID: 3adg
TitleStructure of Arabidopsis HYL1 and its molecular implications for miRNA processing
ComponentsF21M12.9 protein
KeywordsGENE REGULATION / HYL1 / miRNA processing mechanism / RNA BINDING PROTEIN
Function / homology
Function and homology information


nuclear dicing body / ta-siRNA processing / leaf proximal/distal pattern formation / response to cytokinin / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / response to auxin / response to abscisic acid / ribonuclease III activity / miRNA processing ...nuclear dicing body / ta-siRNA processing / leaf proximal/distal pattern formation / response to cytokinin / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / response to auxin / response to abscisic acid / ribonuclease III activity / miRNA processing / pre-miRNA processing / miRNA binding / double-stranded RNA binding / nuclear speck / identical protein binding / nucleus
Similarity search - Function
AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Double-stranded RNA-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYuan, Y.A. / Chen, H.Y.
CitationJournal: Structure / Year: 2010
Title: Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing
Authors: Yang, S.W. / Chen, H.Y. / Yang, J. / Machida, S. / Chua, N.H. / Yuan, Y.A.
History
DepositionJan 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F21M12.9 protein


Theoretical massNumber of molelcules
Total (without water)8,2381
Polymers8,2381
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.388, 37.898, 51.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F21M12.9 protein / Hyponastic leave 1 / Putative uncharacterized protein


Mass: 8238.390 Da / Num. of mol.: 1 / Fragment: HYL1 dsRBD1, UNP residues 15-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HYL1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O04492
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, MgCl2, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 7709 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.032 / Net I/σ(I): 40
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 9 / Num. unique all: 779 / Rsym value: 0.182 / % possible all: 97.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DI2

1di2


Resolution: 1.7→26.25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.52 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.136 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25356 374 4.6 %RANDOM
Rwork0.20695 ---
obs0.20905 7709 98.47 %-
all-8113 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å20 Å2
2---1.57 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms579 0 0 124 703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022592
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.974798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.208571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19623.33327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98115106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.207154
X-RAY DIFFRACTIONr_chiral_restr0.0980.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02448
X-RAY DIFFRACTIONr_nbd_refined0.2210.2284
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.220
X-RAY DIFFRACTIONr_mcbond_it0.931.5367
X-RAY DIFFRACTIONr_mcangle_it1.4742581
X-RAY DIFFRACTIONr_scbond_it2.2293248
X-RAY DIFFRACTIONr_scangle_it3.4064.5217
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 26 -
Rwork0.349 547 -
obs--96.3 %
Refinement TLS params.Method: refined / Origin x: 10.08 Å / Origin y: -6.2199 Å / Origin z: -11.9658 Å
111213212223313233
T-0.1761 Å2-0.0056 Å20.0317 Å2--0.1138 Å20.0287 Å2---0.0711 Å2
L1.7311 °21.0733 °20.6472 °2-6.4613 °21.8826 °2--1.7292 °2
S0.0684 Å °0.0214 Å °-0.1866 Å °-0.0963 Å °-0.0054 Å °-0.4818 Å °-0.0497 Å °-0.0738 Å °-0.063 Å °

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