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- PDB-431d: 5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3' -

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Basic information

Entry
Database: PDB / ID: 431d
Title5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'
ComponentsDNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / EXTENDED HYDRATION SPINE / TRIPLET FORMATION / ATOMIC RESOLUTION / DOUBLE BACKBONE CONFORMATION
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.15 Å
AuthorsVlieghe, D. / Turkenburg, J.P. / Van Meervelt, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: B-DNA at atomic resolution reveals extended hydration patterns.
Authors: Vlieghe, D. / Turkenburg, J.P. / Van Meervelt, L.
#1: Journal: Science / Year: 1996
Title: Parallel and Antiparallel (G-Gc)2 Triple Helix Fragments in a Crystal Structure
Authors: Vlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
History
DepositionOct 9, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,2194
Polymers6,1702
Non-polymers492
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.106, 36.455, 52.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
Temperature: 289. K / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
10.41 mMoligonucleotide1
210.6 mMbuffer1
342.6 mM1MgCl2
44.3 %1
50.22 mMspermine11
640 %MPD12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.15→15 Å / Num. all: 17760 / Num. obs: 17760 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 25
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 11.71 / % possible all: 94.7
Reflection
*PLUS
Num. measured all: 63114
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
SHELXL-93refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: UDJ049 USED AS STARTING MODEL FOR REFINEMENT

Resolution: 1.15→10 Å / Num. parameters: 4811 / Num. restraintsaints: 12226 / Cross valid method: NONE
StereochEM target val spec case: ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES AND ANGLES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS.
Stereochemistry target values: DISTANCES AND ANGLES WITHIN THE BASES WERE RESTRAINED TO TARGET VALUES (TAYLOR AND KENNARD).
Details: SIGMAS USED BOND LENGTHS (TARGET + SIMILAR) 0.03; ANGLE DISTANCES (TARGET + SIMILAR) 0.05; PLANE RESTRAINT FOR BASES 0.02; CHIRAL VOLUME RESTRAINT (A**3) 0.2; ANTI-BUMPING RESTRAINT FOR ...Details: SIGMAS USED BOND LENGTHS (TARGET + SIMILAR) 0.03; ANGLE DISTANCES (TARGET + SIMILAR) 0.05; PLANE RESTRAINT FOR BASES 0.02; CHIRAL VOLUME RESTRAINT (A**3) 0.2; ANTI-BUMPING RESTRAINT FOR SOLVENT MOLECULES 0.03; ISOR RESTRAINT FOR 28 SOLVENTS 0.1, FOR 15 SOLVENTS AND 21 DNA ATOMS 0.05, FOR 3 SOLVENTS 0.025; RIGID- BOND ADP COMPONENTS 0.010; SIMILAR ADP COMPONENTS 0.062
RfactorNum. reflection% reflection
all0.1722 17700 -
obs-16727 96 %
Solvent computationSolvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-222.
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 527.61 / Occupancy sum non hydrogen: 208
Refinement stepCycle: LAST / Resolution: 1.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 416 2 116 534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist0.052
X-RAY DIFFRACTIONs_from_restr_planes0.015
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.155
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.025
X-RAY DIFFRACTIONs_approx_iso_adps0.067
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 4 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.015

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