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- PDB-1zpi: Crystal structure analysis of the minor groove binding quinoliniu... -

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Basic information

Entry
Database: PDB / ID: 1zpi
TitleCrystal structure analysis of the minor groove binding quinolinium quaternary salt SN 8224 complexed with CGCGAATTCGCG
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / B-DNA / dodecamer / minor groove binding complex
Function / homologyChem-SN9 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / refinement / Resolution: 1.6 Å
AuthorsAdams, A. / Leong, C. / Denny, W.A. / Guss, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)(2) at 1.6 and 1.8 Angstrom resolution.
Authors: Adams, A. / Leong, C. / Denny, W.A. / Guss, J.M.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,8614
Polymers7,3272
Non-polymers5342
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.188, 39.868, 65.961
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(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SN9 / 8-METHOXY-1-METHYL-4-(4-(4-(1-METHYLPYRIDINIUM-4-YLAMINO)PHENYLCARBAMOYL)PHENYLAMINO)QUINOLINIUM / SN8224


Mass: 509.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H47N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 7
Details: cacodylate, spermine, magnesium chloride, MPD, pH 7.0, VAPOR DIFFUSION, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2spermine11
3magnesium chloride11
4MPD11
5H2O11
6cacodylate12
7magnesium chloride12
8MPD12
9H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 2004 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 9114 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.0433 / Rsym value: 0.054 / Net I/σ(I): 22.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 841 / Rsym value: 0.389 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: refinement
Starting model: BD0007

Resolution: 1.6→34.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.976 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25832 747 8.2 %RANDOM
Rwork0.22217 ---
all0.225 9114 --
obs0.225 8331 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.529 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å20 Å2
2---1.41 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 522 38 76 636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021631
X-RAY DIFFRACTIONr_bond_other_d0.0020.02279
X-RAY DIFFRACTIONr_angle_refined_deg1.6932.999977
X-RAY DIFFRACTIONr_angle_other_deg1.3533.013678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02314
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023
X-RAY DIFFRACTIONr_nbd_refined0.1810.276
X-RAY DIFFRACTIONr_nbd_other0.2320.2346
X-RAY DIFFRACTIONr_nbtor_refined0.2560.2227
X-RAY DIFFRACTIONr_nbtor_other0.0930.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.070.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it5.9232908
X-RAY DIFFRACTIONr_scangle_it7.0023975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 42 -
Rwork0.335 586 -
obs--93.87 %

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