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- PDB-1pwf: One Sugar Pucker Fits All: Pairing Versatility Despite Conformati... -

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Basic information

Entry
Database: PDB / ID: 1pwf
TitleOne Sugar Pucker Fits All: Pairing Versatility Despite Conformational Uniformity in TNA
Components5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'
KeywordsDNA / A-DNA / Hydrogen Bonding / Nucleic Acid Etiology / Tetrose / Four Carbon Sugar / Nucleic Acid Analogue
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsPallan, P.S. / Wilds, C.J. / Wawrzak, Z. / Krishnamurthy, R. / Eschenmoser, A. / Egli, M.
CitationJournal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2003
Title: Why does TNA cross-pair more strongly with RNA than with DNA? an answer from X-ray analysis.
Authors: Pallan, P.S. / Wilds, C.J. / Wawrzak, Z. / Krishnamurthy, R. / Eschenmoser, A. / Egli, M.
History
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / software
Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3243
Polymers6,1222
Non-polymers2021
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.429, 44.522, 47.332
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*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'


Mass: 3061.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized oligonucleotide
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


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


Mass: 18.015 Da / Num. of mol.: 109 / 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: 39.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Cacodylate, Sodium Chloride, Barium Chloride, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2Sodium Chloride11
3Barium Chloride11
4Spermine tetrahydrochloride11
52-methyl-2,4-pentanediol11
6H2O11
7Sodium Cacodylate12
8Sodium Chloride12
9Barium Chloride12
10H2O12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→30 Å / Num. obs: 18354 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.16→1.2 Å / Rmerge(I) obs: 0.297 / Num. unique all: 1704 / % possible all: 94.5

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPL

1dpl


Resolution: 1.16→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J. Am. Chem. Soc. (1996) 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic ...Stereochemistry target values: L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J. Am. Chem. Soc. (1996) 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J. Am. Chem. Soc. (1996) 118, 519-529; G. Parkinson et al., New Parameters for the Refinement of Nucleic Acid-Containing Structures, Acta Cryst. (1996) D52, 57-64.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 918 -RANDOM
Rwork0.133 ---
obs0.133 17371 100 %-
all-18289 --
Refinement stepCycle: LAST / Resolution: 1.16→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 622 14 109 745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_from_restr_planes0.086
X-RAY DIFFRACTIONs_similar_dist0.04

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