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- PDB-1jtl: The crystal structure of d(GGCCAATTGG) Complexed with Distamycin -

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Basic information

Entry
Database: PDB / ID: 1jtl
TitleThe crystal structure of d(GGCCAATTGG) Complexed with Distamycin
Components5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'
KeywordsDNA / B-DNA double helix / base triplets / minor groove binding / drug / distamycin
Function / homologyDISTAMYCIN A / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsUytterhoeven, K. / Van Meervelt, L.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG).
Authors: Uytterhoeven, K. / Sponer, J. / Van Meervelt, L.
History
DepositionAug 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 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 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'
B: 5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6523
Polymers6,1702
Non-polymers4821
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.289, 36.439, 53.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is synthesized by Oswell DNA Service (Southampton, UK)
#2: Chemical ChemComp-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN


Mass: 481.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MPD, magnesium chloride, cacodylate, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl211
3cacodylate11
4spermine11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
225 mM1dropNaCl
350 mMsodium acetate1droppH5.
40.4 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 4543 / Num. obs: 4223 / % possible obs: 93 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 5 / Redundancy: 4.3 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.08
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 431 / Rsym value: 0.195 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 43223 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.195

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DD0002 used as starting model for refinement

Resolution: 1.85→100 Å / Isotropic thermal model: Isotropic / σ(F): 4 / Stereochemistry target values: user defined
RfactorNum. reflection% reflection
all0.2127 4192 -
obs0.1974 3493 83.3 %
Displacement parametersBiso mean: 33.99 Å2
Refinement stepCycle: LAST / Resolution: 1.85→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 35 74 519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.05
Software
*PLUS
Name: SHELXL / Version: 93 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.2127 / Rfactor obs: 0.1974 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.1974
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.7

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