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- PDB-1dvl: CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COM... -

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Basic information

Entry
Database: PDB / ID: 1dvl
TitleCRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END
Components5'-D(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3'
KeywordsDNA / DRUG BINDING
Function / homologyNETROPSIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShi, K. / Mitra, S.N. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin.
Authors: Shi, K. / Mitra, S.N. / Sundaralingam, M.
History
DepositionJan 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2002Provider: 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
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 5'-D(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3'
B: 5'-D(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3743
Polymers5,9442
Non-polymers4301
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.400, 24.470, 36.310
Angle α, β, γ (deg.)90.00, 110.09, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 2971.911 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic, antivirus*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4 MM DNA (SINGLE STRAND), 0.008M MGCL2, 0.04 M NA CACODYLATE (PH 6.5), 2MM NETROPSIN, VAPOR DIFFUSION, HANGING DROP at 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3MGCL212
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mMDNA1dropsingle strand concentration
20.01 Mcacodylate1droppH6.5
34 mM1dropMgCl2
410 mMammonium bicarbonate1drop
52 mMnetropsin1drop
660 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 1795 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037
Reflection shellResolution: 2.4→2.5 Å
Reflection
*PLUS
Highest resolution: 2.4 Å / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 62.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.196 ---
all0.196 ---
obs0.196 1795 85.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 394 31 31 456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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