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- PDB-305d: SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN TH... -

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Basic information

Entry
Database: PDB / ID: 305d
TitleSIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN THE TETRAGONAL FORM
ComponentsDNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / DOUBLE DRUG IN THE MINOR GROOVE
Function / homologyDISTAMYCIN A / DNA
Function and homology information
MethodX-RAY DIFFRACTION / DIRECT REFINEMENT / Resolution: 2.17 Å
AuthorsChen, X. / Ramakrishnan, B. / Sundaralingam, M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC).
Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Binding of two Distamycin A Molecules in the Minor Groove of an Alternating B-DNA
Authors: Chen, X. / Ramakrishnan, B. / Rao, S.T. / Sundaralingam, M.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Crystal Structures of B-Form DNA-RNA Chimers Complexed with Distamycin
Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionJan 3, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 22, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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.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 1.4Apr 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: DNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,9023
Polymers2,3971
Non-polymers5062
Water72140
1
A: DNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
hetero molecules

A: DNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8056
Polymers4,7932
Non-polymers1,0124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)27.860, 27.860, 58.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 2396.589 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN / Distamycin


Mass: 481.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMDNA1dropsingle strand concentration
220 mMsodium cacodylate1drop
31 mMdistamycin hydrochloride1drop
420 mMmagnesium chloride1drop
51 mg/mlspermine hydrochloride1drop
63 %(v/v)MPD1drop
750 %1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Mar 24, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.17 Å / Num. all: 7996 / Num. obs: 1432 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.056
Reflection
*PLUS
Highest resolution: 2.17 Å / % possible obs: 83 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
XENGEN2data collection
XENGEN2data reduction
X-PLORmodel building
X-PLORrefinement
XENGENV. 2.0data scaling
X-PLORphasing
RefinementMethod to determine structure: DIRECT REFINEMENT
Starting model: GDLB51

Resolution: 2.17→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.174 --
obs0.174 1126 65 %
Displacement parametersBiso mean: 14.8 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.17→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 159 36 40 235
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_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d38.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.1
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.17 Å / Lowest resolution: 8 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg38.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.1

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