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- PDB-196d: CRYSTAL STRUCTURE OF C-T-C-T-C-G-A-G-A-G: IMPLICATIONS FOR THE ST... -

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Basic information

Entry
Database: PDB / ID: 196d
TitleCRYSTAL STRUCTURE OF C-T-C-T-C-G-A-G-A-G: IMPLICATIONS FOR THE STRUCTURE OF THE HOLLIDAY JUNCTION
ComponentsDNA (5'-D(*CP*TP*CP*TP*CP*GP*AP*GP*AP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsGoodsell, D.S. / Grzeskowiak, K. / Dickerson, R.E.
CitationJournal: Biochemistry / Year: 1995
Title: Crystal structure of C-T-C-T-C-G-A-G-A-G. Implications for the structure of the Holliday junction.
Authors: Goodsell, D.S. / Grzeskowiak, K. / Dickerson, R.E.
History
DepositionNov 7, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 27, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_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_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*TP*CP*TP*CP*GP*AP*GP*AP*G)-3')
B: DNA (5'-D(*CP*TP*CP*TP*CP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3308
Polymers6,0902
Non-polymers2406
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.230, 24.320, 40.830
Angle α, β, γ (deg.)90.00, 126.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 278.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CA ACETATE11
4WATER12
5MPD12
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: standing drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.34 mMDNA duplex1drop
2100-250 mMcalcium acetate1drop
315-19 %(v/v)MPD1drop
41
51

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Data collection

DiffractionMean temperature: 93 K
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 4946 / % possible obs: 87 %
Reflection
*PLUS
Highest resolution: 1.7 Å / % possible obs: 87 % / Rmerge(I) obs: 0.056

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.2 4946
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 38 82 524
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it3.6326
X-RAY DIFFRACTIONn_sugar_angle_it4.1416
X-RAY DIFFRACTIONn_phos_bond_it4.5876
X-RAY DIFFRACTIONn_phos_angle_it5.1066
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0210.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0360.035
X-RAY DIFFRACTIONn_phos_bond_d0.0370.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0450.035
X-RAY DIFFRACTIONn_plane_restr0.0210.02
X-RAY DIFFRACTIONn_chiral_restr0.1660.15
X-RAY DIFFRACTIONn_singtor_nbd0.0870.1
X-RAY DIFFRACTIONn_multtor_nbd0.1030.1
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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