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- PDB-3ax1: Molecular insights into miRNA processing by Arabidopsis Serrate -

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Basic information

Entry
Database: PDB / ID: 3ax1
TitleMolecular insights into miRNA processing by Arabidopsis Serrate
ComponentsSerrate RNA effector molecule
KeywordsPROTEIN BINDING / miRNA processing / serrate
Function / homology
Function and homology information


nuclear dicing body / ta-siRNA processing / regulation of meristem development / regulation of adaxial/abaxial pattern formation / shoot system development / nuclear cap binding complex / primary miRNA processing / regulation of alternative mRNA splicing, via spliceosome / RNA splicing / mRNA processing ...nuclear dicing body / ta-siRNA processing / regulation of meristem development / regulation of adaxial/abaxial pattern formation / shoot system development / nuclear cap binding complex / primary miRNA processing / regulation of alternative mRNA splicing, via spliceosome / RNA splicing / mRNA processing / nuclear speck / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleolus / DNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Serrate RNA effector molecule
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.74 Å
AuthorsYuan, Y.A. / Machida, S. / Chen, H.Y.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE
Authors: Machida, S. / Chen, H.Y. / Yuan, Y.A.
History
DepositionMar 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Serrate RNA effector molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8292
Polymers40,7641
Non-polymers651
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.965, 80.663, 112.670
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 Serrate RNA effector molecule


Mass: 40763.832 Da / Num. of mol.: 1 / Fragment: core domain, UNP residues 194-544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SE, At2g27100, T20P8.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZVD0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG4K, Potassium formate, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.2814, 1.2818, 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009
RadiationMonochromator: 360 degree with 1 degree oscillation / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28141
21.28181
31.11
ReflectionResolution: 2.7→50 Å / Num. all: 11900 / Num. obs: 11847 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.74→46.19 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 37.155 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28608 605 4.9 %RANDOM
Rwork0.24293 ---
obs0.24504 11847 97.76 %-
all-11900 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.032 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2--7.98 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.74→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 1 11 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222487
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9563353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24724.32125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.77615462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.981515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021860
X-RAY DIFFRACTIONr_nbd_refined0.2360.21006
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.27
X-RAY DIFFRACTIONr_mcbond_it0.5611.51511
X-RAY DIFFRACTIONr_mcangle_it1.0122383
X-RAY DIFFRACTIONr_scbond_it1.26831089
X-RAY DIFFRACTIONr_scangle_it2.2014.5970
LS refinement shellResolution: 2.742→2.814 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 32 -
Rwork0.402 654 -
obs--72.67 %
Refinement TLS params.Method: refined / Origin x: 13.3249 Å / Origin y: 48.2307 Å / Origin z: 48.445 Å
111213212223313233
T-0.2734 Å2-0.0844 Å2-0.012 Å2--0.1533 Å2-0.0208 Å2---0.1991 Å2
L1.8854 °2-0.4386 °2-0.7261 °2-0.5163 °20.132 °2--2.8378 °2
S-0.0779 Å °0.2047 Å °-0.3773 Å °-0.1318 Å °0.1422 Å °-0.1321 Å °0.4256 Å °-0.2484 Å °-0.0643 Å °

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