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- PDB-2gwa: Crystal Structure of a Complex Formed Between the DNA Holliday Ju... -

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Entry
Database: PDB / ID: 2gwa
TitleCrystal Structure of a Complex Formed Between the DNA Holliday Junction and a Bis-Acridine Molecule.
Components5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
KeywordsDNA / DNA HOLLIDAY JUNCTION BIS-ACRIDINE
Function / homologyChem-A4C / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsBrogden, A.L. / Hopcroft, N.H. / Cardin, C.J. / Searcey, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Ligand bridging of the DNA Holliday junction: molecular recognition of a stacked-X four-way junction by a small molecule.
Authors: Brogden, A.L. / Hopcroft, N.H. / Searcey, M. / Cardin, C.J.
History
DepositionMay 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN HETEROGEN A4C 1 REPRESENTS ONE HALF OF THE LIGAND, THE OTHER HALF IS GENERATED BY THE ...HETEROGEN HETEROGEN A4C 1 REPRESENTS ONE HALF OF THE LIGAND, THE OTHER HALF IS GENERATED BY THE SYMMETRY OPERATION USED TO GENERATE THE BIOLOGICAL UNIT. THE MOLECULE AS A WHOLE LIES ON A CRYSTALLOGRAPHIC AXIS OF TWO-FOLD ROTATIONAL SYMMETRY. HENCE, IN THE ASYMMETRIC UNIT, ONLY HALF THE LIGAND IS PRESENT IN THE COORDINATE FILE SUBMITTED. LINKS ARE PROVIDED BETWEEN SYMMETRY RELATED CX6 ATOMS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
B: 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9914
Polymers6,0902
Non-polymers9012
Water2,324129
1
A: 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
B: 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
hetero molecules

A: 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
B: 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9828
Polymers12,1804
Non-polymers1,8024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)65.224, 25.142, 37.541
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-107-

HOH

21B-182-

HOH

DetailsTHE SECOND PART OF THE BIOLOGICAL UNIT IS GENERATED BY THE SYMMETRY OPERATION: -X, Y, -Z.

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Components

#1: DNA chain 5'-D(*Tp*Cp*Gp*Gp*Tp*Ap*Cp*Cp*Gp*A)-3'


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-A4C / 9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE}


Mass: 698.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H50N8O2
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40mM SODIUM CACODYLATE PH 7.0, 12mM SPERMINE, 10% MPD, WITH 35% MPD RESERVOIR., VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2SPERMINE11
3MPD11
4H2O11
5SODIUM CACODYLATE12
6MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.806 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.806 Å / Relative weight: 1
ReflectionResolution: 1.75→6 Å / Num. all: 4960 / Num. obs: 4045 / % possible obs: 86.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.2 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.1
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 5.2 / Num. unique all: 4960 / % possible all: 86.4

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
MOSFLMdata reduction
RefinementStarting model: PDB ENTRY 1NQS

1nqs


Resolution: 1.75→6 Å / Num. parameters: 2292 / Num. restraintsaints: 1970 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3101 248 5 %RANDOM
Rwork0.268 ---
all0.2769 4960 --
obs0.2769 4045 86.4 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 572
Refinement stepCycle: LAST / Resolution: 1.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 40 129 573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0018
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.092
X-RAY DIFFRACTIONs_approx_iso_adps0

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