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- PDB-365d: STRUCTURAL BASIS FOR G C RECOGNITION IN THE DNA MINOR GROOVE -

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Basic information

Entry
Database: PDB / ID: 365d
TitleSTRUCTURAL BASIS FOR G C RECOGNITION IN THE DNA MINOR GROOVE
ComponentsDNA (5'-D(*CP*CP*AP*GP*GP*(CBR)P*CP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyIMIDAZOLE-PYRROLE POLYAMIDE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKielkopf, C.L. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structural basis for G.C recognition in the DNA minor groove.
Authors: Kielkopf, C.L. / Baird, E.E. / Dervan, P.B. / Rees, D.C.
History
DepositionDec 17, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 5, 1998Provider: 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

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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*GP*(CBR)P*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*(CBR)P*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5494
Polymers6,2502
Non-polymers1,2992
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.396, 38.959, 44.421
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 DNA (5'-D(*CP*CP*AP*GP*GP*(CBR)P*CP*TP*GP*G)-3')


Mass: 3124.888 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-IIP / IMIDAZOLE-PYRROLE POLYAMIDE


Mass: 649.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H41N12O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.934
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop7.5pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
2772vapor diffusion, sitting drop7.5pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CA ACETATE11
4TRIS11
5WATER12
6MPD12
1WATER21
2MPD21
3CA ACETATE21
4TRIS21
5WATER22
6MPD22
Crystal
*PLUS
Density % sol: 34 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Crystal-ID
10.6 mM1
21.3 mM1
312 %1
435 mM1
510 mM1
625 %1

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineID
1
SYNCHROTRONSSRL BL7-12
Detector
TypeIDDetectorDate
RIGAKU RAXIS IIC1IMAGE PLATEApr 4, 1997
MARRESEARCH2IMAGE PLATEMay 3, 1997
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionResolution: 2→18 Å / Num. obs: 4124 / % possible obs: 93.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.027
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 18 Å / % possible obs: 93.9 % / Redundancy: 6.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.857refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→18 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 185 5 %
Rwork0.222 --
obs0.222 3765 91.2 %
Refinement stepCycle: LAST / Resolution: 2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 98 71 573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
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_deg2.2
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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