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- PDB-2gvr: Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65... -

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Basic information

Entry
Database: PDB / ID: 2gvr
TitleCrystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65 A resolution.
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / NUCLEIC ACIDS / DOUBLE HELIX / MINOR GROOVE / CRYSTAL STRUCTURE OF B-DNA / DNA MINOR GROOVE BINDER / DICKERSON AND DREW DODECAMER / D(CGCGAATTCGCG)2 / A2T2 / DNA MINOR GROOVE-LIGAND COMPLEX / DNA-DRUG COMPLEX / DNA HYDRATION / BERENIL AND DNA / BERENIL-DNA COMPLEX / MAGNESIUM-WATER COMPLEX / HYDRATED MAGNESIUM COMPLEX.
Function / homologyBERENIL / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLee, M.P.H. / Parkinson, G.N. / Neidle, S.
CitationJournal: To be Published
Title: Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65 A resolution.
Authors: Neidle, S. / Parkinson, G.N. / Lee, M.P.H.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_auth_seq_id / _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*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)7,6324
Polymers7,3272
Non-polymers3062
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.124, 39.633, 65.728
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 / Details: AT-RICH REGION IN THE GENOME OF ORGANISMS.
#2: Chemical ChemComp-BRN / BERENIL / DIMINAZINE ACETURATE / 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE


Mass: 281.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N7 / Comment: medication*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 285 K / pH: 6.5
Details: MAGNESIUM CHLORIDE, DNA, BERENIL, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 285K, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM CHLORIDE11
2MPD11
3SODIUM CACODYLATE11
4H2O11
5MAGNESIUM CHLORIDE12
6MPD12
7SODIUM CACODYLATE12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 4, 2002 / Details: OSMIC FOCUSING MIRROR SYSTEM
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→17 Å / Num. obs: 7822 / % possible obs: 96.5 % / Observed criterion σ(I): -2 / Redundancy: 4.95 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 58.04
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 12.65 / % possible all: 93.9

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE.

2dbe


Resolution: 1.65→8 Å / Num. parameters: 2363 / Num. restraintsaints: 2511 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.284 756 9.818 %RANDOM
all0.223 7700 --
obs0.219 -95.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 23.59 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 587
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 28 73 587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.01
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.002
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0

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