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- PDB-1dj6: COMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT R... -

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Basic information

Entry
Database: PDB / ID: 1dj6
TitleCOMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT ROOM TEMPERATURE
Components5'-D(*CP*GP*CP*GP*CP*G)-3'
KeywordsDNA / Z-DNA:POLYAMINE COMPLEX / X-RAY CRYSTAL STRUCTURE / POLYAMINE BINDING IN MINOR GROOVE OF Z-DNA
Function / homologyN,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsOhishi, H. / Tomita, K.-i. / Nakanishi, I. / Ohtsuchi, M. / Hakoshima, T. / Rich, A.
CitationJournal: FEBS Lett. / Year: 2002
Title: The crystal structure of N1-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)2, hexamer at room temperature
Authors: Ohishi, H. / Suzuki, K. / Ohtsuchi, M. / Hakoshima, T. / Rich, A.
History
DepositionDec 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 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 / Item: _software.name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9375
Polymers3,6202
Non-polymers3173
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.93, 31.36, 44.62
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-104 / N,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE / TRIENTINE


Mass: 146.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 6

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2MM AMMONIUM SALT OF D(CG)3, 10MM POLYAMINE PA(222) TETRACHLORIDE, 15MM MGCL2, 30MM SODIUM CACODYLATE BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SODIUM CACODYLATE BUFFER11
3POLYAMINE PA(222) TETRACHLORIDE11
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMammonium salt of d(CG)31reservoir
210 mMappropriate polyamine tetrachloride salt1reservoir
315 mM1reservoirMgCl2
430 mMsodium cacodylate1reservoir
520 %MPD1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1→10 Å / Num. all: 11627 / Num. obs: 11212 / % possible obs: 96.4 % / Observed criterion σ(I): 3 / Redundancy: 0.07 % / Biso Wilson estimate: 5.7 Å2 / Net I/σ(I): 40000
Reflection
*PLUS
Num. obs: 10897 / % possible obs: 83.7 % / Num. measured all: 30955

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Processing

Software
NameClassification
DIFDATdata reduction
X-PLORmodel building
SHELXLrefinement
X-PLORphasing
RefinementStarting model: Z-DNA

Resolution: 1→10 Å / Cross valid method: THROUGHOUT / σ(I): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.169 --RANDOM
Rwork0.14 ---
all0.169 11627 --
obs0.165 11212 96.4 %-
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 20 89 349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.001
X-RAY DIFFRACTIONs_angle_d0.01
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS

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