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- PDB-412d: DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-METHYL-[TRI(OX... -

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Basic information

Entry
Database: PDB / ID: 412d
TitleDUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-METHYL-[TRI(OXYETHYL)] RIBONUCLEOSIDE
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(126)P*AP*CP*GP*C)-3')
KeywordsDNA / DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-METHYL-[TRI(OXYETHYL)] RIBONUCLEOSIDE
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsTereshko, V. / Portmann, S. / Tay, E.C. / Martin, P. / Natt, F. / Altmann, K.H. / Egli, M.
CitationJournal: Biochemistry / Year: 1998
Title: Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues.
Authors: Tereshko, V. / Portmann, S. / Tay, E.C. / Martin, P. / Natt, F. / Altmann, K.H. / Egli, M.
History
DepositionJun 30, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 17, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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_type.id / _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: DNA (5'-D(*GP*CP*GP*TP*AP*(126)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(126)P*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4634
Polymers6,4142
Non-polymers492
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.640, 43.620, 45.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*(126)P*AP*CP*GP*C)-3')


Mass: 3207.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.9 Å3/Da / Density % sol: 35.42 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.3 / Details: pH 6.30, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD12
Crystal grow
*PLUS
pH: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMoligonucleotide1drop
230 mMsodium cacodylate1drop
38 mM1dropMgCl2
420 mMspermine tetrahydrochloride1drop
540 %(v/v)MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceTypeID
ROTATING ANODERIGAKU RU2001
2
3
4
Detector
TypeIDDetectorDate
RIGAKU RAXIS II1IMAGE PLATENov 11, 1996
2
3
4
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
3Mx-ray3
4Mx-ray4
Radiation wavelength
IDRelative weight
11
21
31
41
ReflectionResolution: 1.65→21.8 Å / Num. all: 6142 / Num. obs: 6142 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 21.8 Å

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.65→8 Å / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.22 591 10 %RANDOM
Rwork0.189 ---
all0.194 6000 --
obs0.189 5915 96.3 %-
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 24 105 533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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