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- PDB-408d: STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE... -

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Basic information

Entry
Database: PDB / ID: 408d
TitleSTRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA
ComponentsDNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3')
KeywordsDNA / DRUG IN THE DNA MINOR GROOVE
Function / homologyIMIDAZOLE-PYRROLE POLYAMIDE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKielkopf, C.L. / White, S. / Szewczyk, J.W. / Turner, J.M. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
CitationJournal: Science / Year: 1998
Title: A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.
Authors: Kielkopf, C.L. / White, S. / Szewczyk, J.W. / Turner, J.M. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
History
DepositionJun 24, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 19, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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: DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3874
Polymers6,0902
Non-polymers1,2972
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.660, 30.200, 43.460
Angle α, β, γ (deg.)90.00, 123.59, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 3045.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#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.: 87 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM ACETATE11
2MPD11
3TRIS11
4CALCIUM ACETATE12
5MPD12
6TRIS12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 15, 1997
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→16 Å / Num. all: 3417 / Num. obs: 3417 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.038
Reflection
*PLUS
% possible obs: 91.6 % / Num. measured all: 12267
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 82.9 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.242 181 4.6 %
Rwork0.219 --
obs0.219 3402 91 %
all-3583 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 104 87 595
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.29
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
Xplor fileSerial no: 1 / Param file: NOC2ENDO.PARAM / Topol file: IPPP_NODIH.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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