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- PDB-1qc1: CRYSTAL STRUCTURE OF THE SELF-FITTED B-DNA DECAMER D(CCGCCGGCGG) -

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Basic information

Entry
Database: PDB / ID: 1qc1
TitleCRYSTAL STRUCTURE OF THE SELF-FITTED B-DNA DECAMER D(CCGCCGGCGG)
Components5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3'
KeywordsDNA / B-DNA DOUBLE-HELIX / DNA-DNA RECOGNITION
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTimsit, Y. / Moras, D.
Citation
Journal: EMBO J. / Year: 1994
Title: DNA self-fitting: the double helix directs the geometry of its supramolecular assembly
Authors: Timsit, Y. / Moras, D.
#1: Journal: J.Biomol.Struct.Dyn. / Year: 1999
Title: Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations
Authors: Timsit, Y. / Shatzky-Schwartz, M. / Shakked, Z.
History
DepositionMay 14, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0May 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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_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.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
A: 5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1916
Polymers6,0942
Non-polymers974
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.700, 53.700, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-131-

HOH

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Components

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


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30 % MPD, 1MM DNA DUPLEX, 1 MM SPERMINE, 20 MM MAGNESIUM ACETATE, 50 MM CACODYLATE BUFFER, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2SPERMINE11
3MAGNESIUM ACETATE11
4CACODYLATE BUFFER11
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMcacodylate1drop
21 mMdodecamer duplex1drop
31.2 mMspermine tetrahydrochloride1drop
418 mMmagnesium acetate1drop
545 %1reservoir

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Data collection

DiffractionMean temperature: 258 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 1817 / Num. obs: 1817 / Rmerge(I) obs: 0.078
Reflection
*PLUS
Num. measured all: 6367

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
NUCLSQrefinement
RefinementResolution: 2.5→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.147 1698
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 4 85 493
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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