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- PDB-2fii: Crystal Structure Analysis of the B-DNA Dodecamer CGCGAAT-aU-CGCG... -

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Basic information

Entry
Database: PDB / ID: 2fii
TitleCrystal Structure Analysis of the B-DNA Dodecamer CGCGAAT-aU-CGCG, with Incorporated Arabino-Uridin (aU)
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*(UAR)P*CP*GP*CP*G)-3'
KeywordsDNA / Arabinonucleic Acid / Sugar Modifications / B-form DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsEgli, M. / Li, F.
CitationJournal: Biochemistry / Year: 2006
Title: 2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
Authors: Li, F. / Sarkhel, S. / Wilds, C.J. / Wawrzak, Z. / Prakash, T.P. / Manoharan, M. / Egli, M.
History
DepositionDec 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UAR)P*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UAR)P*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3553
Polymers7,3312
Non-polymers241
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.699, 39.915, 65.564
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: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UAR)P*CP*GP*CP*G)-3'


Mass: 3665.365 Da / Num. of mol.: 2 / Mutation: Incorperated arabino-U at position 8 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / pH: 7
Details: Final droplet composition: 0.6 mM oligonucleotide, 20mM sodium cacodylate, 6.3 mM Mg(OAc)2, and 3 mM spermine tetrahydrochloride., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2Mg(OAc)211
3spermine11
4tetrahydrochloride11
5H2O11
6sodium cacodylate12
7Mg(OAc)212
8H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→30 Å / Num. obs: 19780 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.24→1.34 Å / Rmerge(I) obs: 0.168 / % possible all: 99.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB entry BDL084/PDB entry 355D

355d


Resolution: 1.24→30 Å / Num. restraintsaints: 15316 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 985 5 %RANDOM
all0.158 19728 --
obs0.155 ---
Refinement stepCycle: LAST / Resolution: 1.24→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 131 618

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