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- PDB-1cvy: CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO C... -

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Basic information

Entry
Database: PDB / ID: 1cvy
TitleCRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG
Components5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
KeywordsDNA / IMIDAZOLE-PYRROLE POLYAMIDE / DOUBLE DRUG IN MINOR GROOVE / MINOR GROOVE RECOGNITION
Function / homologyIMIDAZOLE-PYRROLE POLYAMIDE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsKielkopf, C.L. / Bremer, R.E. / White, S. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
Authors: Kielkopf, C.L. / Bremer, R.E. / White, S. / Szewczyk, J.W. / Turner, J.M. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
History
DepositionAug 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
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

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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3874
Polymers6,0902
Non-polymers1,2972
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.493, 38.593, 47.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-IPY / IMIDAZOLE-PYRROLE POLYAMIDE / IMIDAZOLE-PYRROLE-PYRROLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE


Mass: 648.736 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H42N11O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: CALCIUM ACETATE, TRIS, MPD, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM ACETATE11
2TRIS11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mMduplex DNA1drop
21.3 mMpolyamide1drop
312 %1drop
435 mMCa acetate1drop
510 mMTris-HCl1drop
625 %MPD1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→17 Å / Num. all: 3618 / Num. obs: 3618 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.8
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.074 / % possible all: 94.2
Reflection
*PLUS
Num. measured all: 21424
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 7.4

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.15→17 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 144 5 %RANDOM
Rwork0.229 ---
obs0.229 3618 97.2 %-
all-3618 --
Refinement stepCycle: LAST / Resolution: 2.15→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 94 52 550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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