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- PDB-358d: CRYSTAL STRUCTURE OF THE 2:1 NETROPSIN-DNA DECAMER D(CBRCCCCIIIII... -

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Basic information

Entry
Database: PDB / ID: 358d
TitleCRYSTAL STRUCTURE OF THE 2:1 NETROPSIN-DNA DECAMER D(CBRCCCCIIIII) COMPLEX WITH END-TO-END BINDING
ComponentsDNA (5'-D(*CP*(CBR)P*CP*CP*CP*IP*IP*IP*IP*I)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyNETROPSIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMitra, S.N. / Chen, X. / 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
DepositionOct 20, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0May 7, 2000Provider: 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 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*(CBR)P*CP*CP*CP*IP*IP*IP*IP*I)-3')
B: DNA (5'-D(*CP*(CBR)P*CP*CP*CP*IP*IP*IP*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9634
Polymers6,1022
Non-polymers8612
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.130, 32.130, 143.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


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


Mass: 430.464 Da / Num. of mol.: 2 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Crystal grow
*PLUS
Temperature: 291 K / pH: 6 / Method: vapor diffusion, hanging drop
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

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Data collection

DiffractionMean temperature: 293 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→26 Å / Num. obs: 1746 / % possible obs: 60.3 % / Observed criterion σ(I): 4 / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 3.14
Reflection shellResolution: 2.5→2.67 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 3.1 / % possible all: 13.6
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 26 Å / % possible obs: 60.3 % / Observed criterion σ(I): 4 / Biso Wilson estimate: 22.8 Å2
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.67 Å / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
MSCdata reduction
RefinementStarting model: D(CCCCCIIIII)

Resolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.298 163 10 %
Rwork0.211 --
obs0.211 1667 60.3 %
Displacement parametersBiso mean: 17.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 394 64 38 496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.69
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM_ND.DNATOP_NDBX.DNA
X-RAY DIFFRACTION2PARAM.NETTOPOLOGY.NET
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.69
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38

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