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- PDB-474d: A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D... -

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Basic information

Entry
Database: PDB / ID: 474d
TitleA NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2
ComponentsDNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
KeywordsDNA / B-DNA/RNA / DOUBLE HELIX / DOUBLE DRUG IN MINOR GROOVE / COMPLEXED WITH DRUG / MODIFIED / MISMATCHED
Function / homologyNETROPSIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsChen, X. / Rao, S.T. / Sekar, K. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2.
Authors: Chen, X. / Mitra, S.N. / Rao, S.T. / Sekar, K. / Sundaralingam, M.
History
DepositionJan 14, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
B: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
C: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
D: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9258
Polymers12,2034
Non-polymers1,7224
Water68538
1
A: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
B: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9634
Polymers6,1022
Non-polymers8612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
D: DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9634
Polymers6,1022
Non-polymers8612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.660, 32.770, 37.710
Angle α, β, γ (deg.)86.01, 84.37, 68.90
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')


Mass: 3050.807 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.58 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NETROPSIN11
3NA CACODYLATE11
4[CO(NH3)6]CL311
5WATER12
6NETROPSIN12
7NA CACODYLATE12
8[CO(NH3)6]CL312
9MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 291 K / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.3 mMoligonucleotide1drop
20.3 mMnetropsin1drop
30.4 mMsodium cacodylate1drop
40.06 mMcobaltic hexamine chloride1drop
560 %MPD1reservoir
61
71
81
91

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 8747 / % possible obs: 73 % / Observed criterion σ(I): 1.4 / Redundancy: 2.04 % / Rmerge(I) obs: 0.045
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / Num. obs: 4284 / % possible obs: 73 % / Observed criterion σ(I): 1.4 / Redundancy: 2.04 % / Rmerge(I) obs: 0.061

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MSCdata reduction
MSCdata scaling
RefinementResolution: 2.4→8 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.273 193 5 %
Rwork0.19 --
obs-3883 73 %
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 788 128 38 954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / % reflection Rfree: 5 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81

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