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- PDB-3tok: Assaying the energies of biological halogen bonds. -

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Basic information

Entry
Database: PDB / ID: 3tok
TitleAssaying the energies of biological halogen bonds.
Components
  • DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
  • DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3')
KeywordsDNA / DNA Holliday Junction
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsCarter, M. / Ho, P.S.
CitationJournal: CRYST.GROWTH DES. / Year: 2011
Title: Assaying the Energies of Biological Halogen Bonds
Authors: Carter, M. / Ho, P.S.
History
DepositionSep 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_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_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*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1143
Polymers6,0912
Non-polymers231
Water2,306128
1
A: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2286
Polymers12,1824
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3050 Å2
ΔGint-32 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.36, 24.60, 37.41
Angle α, β, γ (deg.)90.00, 110.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-207-

HOH

21B-274-

HOH

DetailsThe asymmetric unit contains two DNA strands. The biological unit is deposited as four strands, containing two pairs of symmetry related alternative conformations

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Components

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


Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#2: DNA chain DNA (5'-D(*CP*CP*GP*GP*TP*AP*TP*CP*GP*G)-3')


Mass: 3061.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25mM Sodium Calcodylate, 10mM Calcuim Chloride, 1.1mM Spermine, and 0.35mM of each DNA strand, pH 7.0, vapor diffusion, sitting drop,temperature 298K, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 24, 2009
RadiationMonochromator: Rosenbaum-rock SI(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 10026 / % possible obs: 97.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
HKL-2000data collection
EPMRphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ORG

2org


Resolution: 1.74→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2913 297 -Random
Rwork0.2339 ---
all0.2357 5886 --
obs0.22042 5299 88.8 %-
Refinement stepCycle: LAST / Resolution: 1.74→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 1 128 533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.343
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.9
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.74→1.84 Å

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