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- PDB-2i2i: Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex. -

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Basic information

Entry
Database: PDB / ID: 2i2i
TitleCrystal structure of the DB293-D(CGCGAATTCGCG)2 complex.
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / B-TYPE DNA DODECAMER WITH COMPOUND DB 293.
Function / homologyChem-MBC / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsLee, M.P.H. / Neidle, S.
CitationJournal: To be Published
Title: Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex.
Authors: Lee, M.P.H. / Neidle, S.
History
DepositionAug 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 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_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

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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)7,6954
Polymers7,3272
Non-polymers3692
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.176, 39.762, 65.750
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MBC / 2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-FURYL)-1H-BENZIMIDAZOLE-5-CARBOXIMIDAMIDE / DB 293


Mass: 344.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / pH: 7
Details: MAGNESIUM CHLORIDE, DNA DODECAMER, MPD, COMPOUND DB 293, SODIUM CACODYLATE BUFFER., pH 7.0, VAPOR DIFFUSION, HANGING DROP, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM CHLORIDE11
2MPD11
3SODIUM CACODYLATE11
4H2O11
5SODIUM CACODYLATE12
6MAGNESIUM CHLORIDE12
7H2O12

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 7, 2006 / 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: 1.63→25.34 Å / Num. obs: 8262 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 3.36 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 16
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 3.7 / % possible all: 99.5

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Processing

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

2dbe


Resolution: 1.63→8 Å / Num. parameters: 2379 / Num. restraintsaints: 2537 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 799 9.76 %RANDOM
all0.228 8184 --
obs0.22 -89 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 594
Refinement stepCycle: LAST / Resolution: 1.63→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 33 75 594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.015
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.007
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0

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