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- PDB-1puy: 1.5 A resolution structure of a synthetic DNA hairpin with a stil... -

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Basic information

Entry
Database: PDB / ID: 1puy
Title1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker
Components5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3'
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEgli, M. / Tereshko, V. / Murshudov, G. / Sanishvili, R. / Liu, X. / Lewis, F.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Face-to-face and edge-to-face pi-pi interactions in a synthetic DNA hairpin with a stilbenediether linker
Authors: Egli, M. / Tereshko, V. / Mushudov, G.N. / Sanishvili, R. / Liu, X. / Lewis, F.D.
History
DepositionJun 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_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_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3'
B: 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1897
Polymers8,0682
Non-polymers1225
Water3,063170
1
A: 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1074
Polymers4,0341
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0823
Polymers4,0341
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.890, 41.860, 51.100
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(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3'


Mass: 4033.808 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic construct
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 298 K / pH: 6.3
Details: MPD, magnesium chloride, cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.30
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium chloride11
3cacodylateCacodylic acid11
4H2O11
5MPD12
6magnesium chloride12
7H2O12
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMDNA1dropSd2-linked
240 mM1dropMgCl2
38 %MPD1drop
440 mMsodium cacodylate1droppH6.
540 %1reservoir
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: APS-1 / Detector: CCD / Date: May 1, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→14.95 Å / Num. obs: 10079 / % possible obs: 93.9 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Num. obs: 9590 / Redundancy: 6.8 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.539 Å / Num. unique obs: 637

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.355 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 489 4.9 %RANDOM
Rwork0.204 ---
obs0.206 9590 93.9 %-
all-9590 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2--2.69 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 536 5 170 711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02598
X-RAY DIFFRACTIONr_bond_other_d0.0030.02264
X-RAY DIFFRACTIONr_angle_refined_deg1.9872.09892
X-RAY DIFFRACTIONr_angle_other_deg1.1352654
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_restr0.0770.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1410.255
X-RAY DIFFRACTIONr_nbd_other0.2670.2328
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1590.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.2323598
X-RAY DIFFRACTIONr_scangle_it2.9544.5892
X-RAY DIFFRACTIONr_rigid_bond_restr1.6532598
X-RAY DIFFRACTIONr_sphericity_free2.7942175
X-RAY DIFFRACTIONr_sphericity_bonded2.4062536
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 30
Rwork0.174 637
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07860.061-0.07480.3326-0.04460.1001-0.00280.0516-0.04280.05140.0041-0.02820.01880.03-0.00140.0991-0.0038-0.00820.0004-0.00430.07189.41242.13787.9253
2-0.05170.3557-0.63340.1413-0.53112.22580.0805-0.03510.02990.04230.04930.0526-0.06280.0688-0.12980.089800.01150.0134-0.00340.082522.79191.614420.0751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 141 - 13
2X-RAY DIFFRACTION2BB1 - 141 - 13
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.176

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