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- PDB-4e8u: Crystal structure of Arabidopsis IDN2 XS domain along with a smal... -

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Basic information

Entry
Database: PDB / ID: 4e8u
TitleCrystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region
ComponentsPutative uncharacterized protein T8P19.180
KeywordsRNA BINDING PROTEIN / XS domain / RNA directed DNA methylation / RNA
Function / homology
Function and homology information


gene silencing by siRNA-directed DNA methylation / regulation of double-strand break repair via homologous recombination / response to cadmium ion / RNA binding
Similarity search - Function
XS domain / Factor of DNA methylation 1-5/IDN2 , domain XH / XS domain / Zinc finger-XS domain / XS domain superfamily / Factor of DNA methylation 1-5/IDN2 / XS domain / XH domain / XS zinc finger domain / Alpha-Beta Plaits ...XS domain / Factor of DNA methylation 1-5/IDN2 , domain XH / XS domain / Zinc finger-XS domain / XS domain superfamily / Factor of DNA methylation 1-5/IDN2 / XS domain / XH domain / XS zinc finger domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein INVOLVED IN DE NOVO 2 / Protein INVOLVED IN DE NOVO 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD (using a smaller construct), molecular replacement / Resolution: 2.701 Å
AuthorsSimanshu, D.K. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.
Authors: Ausin, I. / Greenberg, M.V. / Simanshu, D.K. / Hale, C.J. / Vashisht, A.A. / Simon, S.A. / Lee, T.F. / Feng, S. / Espanola, S.D. / Meyers, B.C. / Wohlschlegel, J.A. / Patel, D.J. / Jacobsen, S.E.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Putative uncharacterized protein T8P19.180
C: Putative uncharacterized protein T8P19.180
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6486
Polymers39,2642
Non-polymers3844
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-26 kcal/mol
Surface area19100 Å2
MethodPISA
2
A: Putative uncharacterized protein T8P19.180
C: Putative uncharacterized protein T8P19.180
hetero molecules

A: Putative uncharacterized protein T8P19.180
C: Putative uncharacterized protein T8P19.180
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,29712
Polymers78,5284
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area8990 Å2
ΔGint-64 kcal/mol
Surface area33440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.370, 207.022, 119.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-408-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 6:170 )A6 - 170
211chain C and (resseq 6:170 )C6 - 170

NCS oper: (Code: given
Matrix: (0.999664, -0.003911, -0.02561), (0.003784, 0.99998, -0.005006), (0.025629, 0.004907, 0.999659)
Vector: -23.7708, -3.94878, -60.612598)

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Components

#1: Protein Putative uncharacterized protein T8P19.180


Mass: 19632.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IDN2, T8P19.180 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9SMN2, UniProt: Q8VZ79*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2010
Details: Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry
RadiationMonochromator: Cryo-Cooled Si(111) double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18040 / % possible obs: 99 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.087 / Χ2: 2.453 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.810.40.54717211.283196.3
2.8-2.9110.40.43217641.344198.2
2.91-3.0410.50.31317811.511199.8
3.04-3.210.70.22117891.626199.8
3.2-3.410.60.15618021.863199.8
3.4-3.6610.40.1117992.256199.8
3.66-4.0310.30.08618192.449199.9
4.03-4.62100.06518203.022199.6
4.62-5.819.90.05718433.282199.6
5.81-509.60.04519026.021197.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD (using a smaller construct), molecular replacement
Resolution: 2.701→29.888 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.36 / Cross valid method: R-Free / σ(F): 0.1 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3058 825 5.09 %Random
Rwork0.2512 ---
obs0.254 16224 88.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.948 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 169.8 Å2 / Biso mean: 82.6751 Å2 / Biso min: 18.43 Å2
Baniso -1Baniso -2Baniso -3
1-42.5068 Å2-0 Å2-0 Å2
2---22.0526 Å2-0 Å2
3----20.4542 Å2
Refinement stepCycle: LAST / Resolution: 2.701→29.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 20 25 2640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082688
X-RAY DIFFRACTIONf_angle_d1.1753644
X-RAY DIFFRACTIONf_chiral_restr0.069387
X-RAY DIFFRACTIONf_plane_restr0.004469
X-RAY DIFFRACTIONf_dihedral_angle_d17.05982
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1265X-RAY DIFFRACTIONPOSITIONAL0.072
12C1265X-RAY DIFFRACTIONPOSITIONAL0.072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.701-2.87050.44381070.30312014212171
2.8705-3.0920.28931320.27662373250582
3.092-3.40270.37521420.25432549269190
3.4027-3.89420.29921640.24412686285094
3.8942-4.90280.26211290.20472818294796
4.9028-29.88940.27961510.24522959311097
Refinement TLS params.Method: refined / Origin x: 16.4628 Å / Origin y: 23.7646 Å / Origin z: 72.2328 Å
111213212223313233
T0.4678 Å2-0.0145 Å2-0.0565 Å2-0.1913 Å2-0.0305 Å2--0.2166 Å2
L-0.02 °20.0335 °2-0.1127 °2-0.3361 °2-0.0415 °2--0.0989 °2
S-0.1491 Å °-0.056 Å °0.0859 Å °0.098 Å °0.041 Å °-0.0112 Å °-0.4008 Å °-0.0732 Å °0.0798 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA124 - 289
2X-RAY DIFFRACTION1allC125 - 289
3X-RAY DIFFRACTION1allC1 - 303
4X-RAY DIFFRACTION1allA1 - 413

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