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- PDB-3i1d: Distinct recognition of three-way DNA junctions by the two enanti... -

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Basic information

Entry
Database: PDB / ID: 3i1d
TitleDistinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate')
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / Drug-DNA complex / 3-way junction / DNA structure recognition
Function / homology: / Chem-NPM / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBoer, D.R. / Uson, I. / Hannon, M.J. / Coll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders.
Authors: Boer, D.R. / Kerckhoffs, J.M. / Parajo, Y. / Pascu, M. / Uson, I. / Lincoln, P. / Hannon, M.J. / Coll, M.
History
DepositionJun 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_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*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,34217
Polymers3,6182
Non-polymers3,72315
Water905
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)9,31821
Polymers5,4283
Non-polymers3,89118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
2
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)12,70630
Polymers5,4283
Non-polymers7,27927
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
3
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)20,89548
Polymers10,8556
Non-polymers10,04042
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation18_654-x+7/4,z+1/4,y-1/41
crystal symmetry operation21_645z+5/4,y-1/4,-x+3/41
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.970, 74.970, 74.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Details1 - First cylinder-bound 3-way junction with continuous DNA strands around NPM ligands of chain I, symops on chain A: Rot = [-Z+1/2, -X, Y+1/2], Trans = [0 0 -1] Rot = [-Y, Z+1/2, -X+1/2], Trans = [1 0 -1] / 2 - Second cylinder-bound 3-way junction with continuous DNA strands around NPM ligands of chain K, symops on chain B: Rot = [Y+1/2, -Z+1/2, -X], Trans = [0 0 0] Rot = [-Z, X+1/2, -Y+1/2], Trans = [1 0 0] / 3 - Cylinder-bound 3-way junction with discontinuous DNA strands around NPM ligands of chain J, symops on : chain A Rot = [-Z+1/2, -X, Y+1/2], Trans = [0 0 -1] Rot = [Z+1/4, Y+3/4, -X+3/4], Trans = [1 -1 -1] Rot = [-X+3/4, Z+1/4, Y+3/4], Trans = [0 0 -1] chain B Rot = [-Z, X+1/2, -Y+1/2], Trans = [1 0 0]

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Components

#1: DNA chain 5'-D(*CP*GP*TP*AP*CP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by Biomer (Ulm, Germany)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-NPM / N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE / 1,1-BIS(N-(4-PHENYL)-2-PYRIDYLCARBOXALDIMINE)METHANE


Mass: 376.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C25H20N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTHORS STATE THAT THE EXTENSIVE DISORDER OF THE DNA-BOUND CYLINDER MOLECULES AROUND SYMMETRY- ...AUTHORS STATE THAT THE EXTENSIVE DISORDER OF THE DNA-BOUND CYLINDER MOLECULES AROUND SYMMETRY-RELATED SITES IS REAL SINCE IT ALSO OCCURS WHEN THE STRUCTURE IS REFINED IN LOWER-SYMMETRY SPACE GROUPS (E.G. P1) AGAINST APPROPRIATELY MERGED DATA, THAT THEREFORE THE DEPOSITED SPACE GROUP IS CORRECT AND THAT THE CURRENT MODEL IS THE CORRECT WAY TO DESCRIBE THE STRUCTURE.
Nonpolymer detailsTHERE ARE THREE LIGAND CLUSTERS OF NPM IN THE STRUCTURE, EACH HAVING WITH PSEUDO-3-FOLD SYMMETRY ...THERE ARE THREE LIGAND CLUSTERS OF NPM IN THE STRUCTURE, EACH HAVING WITH PSEUDO-3-FOLD SYMMETRY AND CONSISTING OF THREE NPM COMPOUNDS COORDINATED BY TWO FE(2+) IONS. GROUP 1 INCLUDES RESIDUES A101, A102, A203, A204, A205; GROUP 2 B7, B8, B9, B10, B102; AND GROUP 3 A7, B102, B203, B204, B205. ALTHOUGH ALL GROUPS CONSIST OF FE(2+) IONS AND THE SAME CHEMICAL COMPONENT NPM, THE OVERALL TOPOLOGY OF THE THREE GROUPS ARE DIFFERENT, WITH GROUP 1 AND 2 AS ONE TYPE (THE M HELICAL ENANTIOMER), AND GROUP 3 AS THE OTHER (THE P HELICAL ENANTIOMER)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM Magnesium acetate, 50 mM Sodium cacodylate, 1.3 M Lithium sulfate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium acetate11
2Sodium cacodylate11
3Lithium sulfate11
4Magnesium acetate12
5Sodium cacodylate12
6Lithium sulfate12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9763
SYNCHROTRONESRF BM1621.739
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 5, 2005
ADSC QUANTUM 210r2CCDMay 5, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single Silicon (111)SINGLE WAVELENGTHMx-ray1
2Si(111) double-crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.7391
ReflectionResolution: 2.5→18.182 Å / Num. all: 2766 / Num. obs: 2766 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 15.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 33.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 4.08 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→18.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.398 / SU ML: 0.311 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.584 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25918 127 4.6 %RANDOM
Rwork0.24482 ---
obs0.24546 2629 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.027 Å2
Refinement stepCycle: LAST / Resolution: 2.5→18.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 267 5 512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0833779
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.110.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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_it2.1313592
X-RAY DIFFRACTIONr_scangle_it3.534.5779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 9 -
Rwork0.508 170 -
obs--100 %

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