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- PDB-100d: CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(... -

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Basic information

Entry
Database: PDB / ID: 100d
TitleCRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING
ComponentsDNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologySPERMINE / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBan, C. / Ramakrishnan, B. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 1994
Title: Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing.
Authors: Ban, C. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionDec 5, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3')
B: DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3603
Polymers6,1582
Non-polymers2021
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.980, 40.770, 44.840
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/RNA hybrid DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3')


Mass: 3078.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.89 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMdecamer duplex1drop
240 mMsodium cacodylate1drop
32.0 mMspermine tetrachloride1drop
445 %MPD1reservoir
51
61

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 9305 / Num. obs: 2365
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.058

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.9→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.145 -
obs0.145 2314
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 14 67 489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.8
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
Refinement
*PLUS
σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_dihedral_angle_deg32
X-RAY DIFFRACTIONx_improper_angle_deg2.1

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