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- PDB-334d: DEFINING GC-SPECIFICITY IN THE MINOR GROOVE: SIDE-BY-SIDE BINDING... -

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Basic information

Entry
Database: PDB / ID: 334d
TitleDEFINING GC-SPECIFICITY IN THE MINOR GROOVE: SIDE-BY-SIDE BINDING OF THE DI-IMIDAZOLE LEXITROPSIN TO C-A-T-G-G-C-C-A-T-G
ComponentsDNA (5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDIIMIDAZOLE LEXITROPSIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKopka, M.L. / Goodsell, D.S. / Dickerson, R.E.
CitationJournal: Structure / Year: 1997
Title: Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G.
Authors: Kopka, M.L. / Goodsell, D.S. / Han, G.W. / Chiu, T.K. / Lown, J.W. / Dickerson, R.E.
History
DepositionMay 22, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 29, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 21, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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: DNA (5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3')
B: DNA (5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8555
Polymers6,0902
Non-polymers7653
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.654, 42.643, 34.684
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*AP*TP*GP*GP*CP*CP*AP*TP*G)-3')


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-DIM / DIIMIDAZOLE LEXITROPSIN


Mass: 362.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N9O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.14 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACL211
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.45 mMduplex DNA1drop
20.90 mMDIM1drop
312 mM1dropCaCl2
47 mMspermine hydrochloride1drop
515 %(v/v)MPD1drop
645 %1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1993 / Details: MIRROR MSC-YALE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. obs: 4895 / % possible obs: 93 % / Biso Wilson estimate: 21.41 Å2 / Rmerge(I) obs: 0.0374
Reflection shellResolution: 1.8→1.85 Å / % possible all: 91.9
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / % possible obs: 93 % / Observed criterion σ(F): 1

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Processing

Software
NameClassification
X-PLORmodel building
NUCLSQrefinement
MSCdata reduction
MSCdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AN IDEAL HELIX RMS FIT TO BDJ057

Resolution: 1.8→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 4895 92 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 57 58 519
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it4.0266
X-RAY DIFFRACTIONn_sugar_angle_it4.6646
X-RAY DIFFRACTIONn_phos_bond_it4.8586
X-RAY DIFFRACTIONn_phos_angle_it4.6546
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0260.03
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0390.027
X-RAY DIFFRACTIONn_phos_bond_d0.050.04
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0690.05
X-RAY DIFFRACTIONn_plane_restr0.0160.02
X-RAY DIFFRACTIONn_chiral_restr0.1460.15
X-RAY DIFFRACTIONn_singtor_nbd0.0850.1
X-RAY DIFFRACTIONn_multtor_nbd0.1040.1
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / σ(F): 1 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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