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- PDB-192d: RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG) -

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Basic information

Entry
Database: PDB / ID: 192d
TitleRECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)
ComponentsDNA (5'-D(*CP*CP*GP*CP*GP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / FLIPPED-OUT BASES
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsMalinina, L. / Urpi, L. / Salas, X. / Huynh-Dinh, T. / Subirana, J.A.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Recombination-like structure of d(CCGCGG).
Authors: Malinina, L. / Urpi, L. / Salas, X. / Huynh-Dinh, T. / Subirana, J.A.
History
DepositionSep 22, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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 (5'-D(*CP*CP*GP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6433
Polymers3,6202
Non-polymers231
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.330, 44.040, 38.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-13-

NA

21B-44-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*CP*GP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2 Å3/Da / Density % sol: 38.43 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4TETRA-ARGININE11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.83 mMhexanucleotide1drop
22.8 mMspermine1drop
30.6 mMtetra arginine1drop
418 mMsodium ccacodylate1drop
520 %(v/v)MPD1drop
645 %MPD1reservoir
71

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: OTHER / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.92 Å / Num. all: 13022 / Num. obs: 2297
Reflection
*PLUS
Highest resolution: 1.92 Å / % possible obs: 96.5 % / Redundancy: 5.7 % / Num. measured all: 13022 / Rmerge(I) obs: 0.056

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.92→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 2297 96.5 %
Refine Biso
ClassRefine-ID
ALL ATOMSX-RAY DIFFRACTION
ALL WATERSX-RAY DIFFRACTION
Refinement stepCycle: LAST / Resolution: 1.92→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 274 1 114 389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.28
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
Highest resolution: 1.92 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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