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- PDB-1p1y: Crystal structure of a continuous three-dimensional DNA lattice f... -

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Basic information

Entry
Database: PDB / ID: 1p1y
TitleCrystal structure of a continuous three-dimensional DNA lattice from d(GGACAGATGGGAG)
Components5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'
KeywordsDNA / continuous three-dimensional dna lattice / parallel-stranded base pairs
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPaukstelis, P.J. / Nowakowski, J. / Birktoft, J.J. / Seeman, N.C.
CitationJournal: Chem.Biol. / Year: 2004
Title: Crystal structure of a continuous three-dimensional DNA lattice.
Authors: Paukstelis, P.J. / Nowakowski, J. / Birktoft, J.J. / Seeman, N.C.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 2, 2011Group: Non-polymer description
Revision 1.4Feb 14, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
X: 5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2742
Polymers4,2491
Non-polymers241
Water41423
1
X: 5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'
hetero molecules

X: 5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5484
Polymers8,4992
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_435-x-1,-y-2,z1
Unit cell
Length a, b, c (Å)40.630, 40.630, 55.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: DNA chain 5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'


Mass: 4249.451 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop
Details: magnesium formate, mpd, lithium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium formate11
2mpd11
3LiCl11
4mpd12
5LiCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.92002 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92002 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 5957 / Num. obs: 3066 / % possible obs: 99 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 20.7
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 13.76 / Num. unique all: 307 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→35.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.627 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.163 / ESU R Free: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.23256 161 5.3 %RANDOM
Rwork0.20332 ---
all0.20485 2907 --
obs0.20485 2870 98.7 %-
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: 39.727 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0.75 Å20 Å2
2---1.5 Å20 Å2
3---2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 257 1 23 281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1333451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02142
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3810.274
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 16
Rwork0.228 217

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